diff --git a/README.md b/README.md
index ba1d0e9..c7f9a9d 100644
--- a/README.md
+++ b/README.md
@@ -34,7 +34,8 @@ now sets the home position.  Zooming and movement keys now work in the
 second view.  Perfectly duplicates lines are now culled during DRC by
 the `V` key.  Rows and columns are now stored as sorted lists intead
 of sets.  Rows and columns are now in a consistent order in the file
-export.  30% speed-up on bit marking.
+export.  Performance boosts in bit marking, background bit marking
+and alignment.
 
 2024-07-14 -- Fixes crash when deleting a double-selected item.  Delete
 and backspace now delete objects like `D`.  Multiple disassemblers.
diff --git a/main.cpp b/main.cpp
index 4085667..61139fb 100644
--- a/main.cpp
+++ b/main.cpp
@@ -147,6 +147,7 @@ int main(int argc, char *argv[]){
         //Don't print anything because the function takes care of it for us.
         mrt.enableVerbose();
     }
+    a.processEvents();
 
     mrt.show();
     for(int i=0; i<args.count(); i++)
@@ -215,12 +216,13 @@ int main(int argc, char *argv[]){
         qDebug()<<"Stressing the loaded project.";
         for(int i=0; i<10; i++){
             qDebug()<<"Round"<<i<<"of bit clearing.";
-            mrt.clearBits();
-            a.processEvents();
+            mrt.clearBits(true);
+            //a.processEvents();
+            assert(mrt.bitcount==0);
             qDebug()<<"Round"<<i<<"of bit marking.";
-            mrt.markBits();
-            a.processEvents();
-            qDebug()<<"Round"<<i<<"of bit aligning.";
+
+            while(!mrt.markBits(false))
+                a.processEvents();
             mrt.markBitTable();
             a.processEvents();
         }
diff --git a/maskromtool.cpp b/maskromtool.cpp
index e91c962..ee43765 100644
--- a/maskromtool.cpp
+++ b/maskromtool.cpp
@@ -669,6 +669,7 @@ void MaskRomTool::keyPressEvent(QKeyEvent *event){
     case Qt::Key_F:
         if(shift && !ctrl && !alt){ //Force a Bit
             markUndoPoint();
+            fixBit(scene->scenepos);
             statusBar()->showMessage(tr("Forced a bit."));
         }
         break;
@@ -706,8 +707,7 @@ void MaskRomTool::keyPressEvent(QKeyEvent *event){
                     duplicateItem(item);
                 }
             }
-            //Update bits when done.
-            markBits(false);
+            //Don't bother forcing an update.  That can come later.
         }else if(none){      //Delete
             foreach(QGraphicsItem* item, scene->selection){
                 removeItem(item);
@@ -770,13 +770,10 @@ void MaskRomTool::keyPressEvent(QKeyEvent *event){
 
     //These operate on the loaded data.
     case Qt::Key_M:  //Mark Bits.
-        markBits(true);
-        if(asciiDialog.isVisible())
-            on_asciiButton_triggered();
-        statusBar()->showMessage(tr("Marked bits."));
+        //This kicks off the state machine to redraw all bits.
+        clearBits(false);
         if(shift){
             on_actionHexView_triggered();
-            statusBar()->showMessage(tr("Decoded bits."));
         }
         break;
     }
@@ -1422,7 +1419,7 @@ void MaskRomTool::markLine(RomLineItem* line){
      * rather than just one type.
      */
 
-    foreach(QGraphicsItem* item, scene->collidingItems(line)){
+    if(!line->marked) foreach(QGraphicsItem* item, scene->collidingItems(line)){
         //We are only looking for columns that collide with rows here.  All other collisions are irrelevant.
         if(line->linetype==RomLineItem::LINEROW
                 && item->type()==item->UserType+1  //Is the colliding item a column?
@@ -1437,6 +1434,8 @@ void MaskRomTool::markLine(RomLineItem* line){
         }
     }
 
+    line->marked=true;
+
     updateCrosshairAngle(line);
 }
 
@@ -1518,35 +1517,39 @@ void MaskRomTool::moveList(QList<QGraphicsItem*> list, QPointF offset){
 }
 
 //Mark up all of the bits where rows and columns collide.
-void MaskRomTool::markBits(bool full){
+bool MaskRomTool::markBits(bool full){
     bool bitswerevisible=bitsVisible;
     bool lineswerevisible=linesVisible;
+    uint64_t count=0;
+
+    state=STATE_MARKING;
 
-    //Exit early if there's nothing to do.
-    if(!markingdirty) return;
+    //Exit quick and early if there's nothing to do.
+    //This is needed because partial updates are called in rendering loop.
+    if(!markingdirty) return true;
 
     if(!lineswerevisible)
         setLinesVisible(true);
 
-    //We're blowing away the alignment here, will need to rebuild it later.
-    alignmentdirty=true;
-
-    //First we remove all the old bits.  This is very slow.
-    if(verbose) qDebug()<<"Clearing bits.";
-    clearBits();
-
-    bitcount=0;
     setBitsVisible(false);
 
     //Mark every line collision.
-    if(verbose) qDebug()<<"Marking bits.";
-    foreach (RomLineItem* line, cols)
+    foreach (RomLineItem* line, cols){
+        if(!line->marked && count++>50 && !full){
+            //Show the bits if--and only if--we've set that style.
+            setBitsVisible(bitswerevisible);
+            //Same for the lines.
+            setLinesVisible(lineswerevisible);
+            return false;
+        }
+        if(!line->marked) alignmentdirty=true;
         markLine(line);
-    if(verbose) qDebug()<<"Sorting bits.";
-    sortBits();
+    }
 
+    //Now our marking is clean, if unsorted.
+    markingdirty=false;
+    sortBits();
     //Mark all the fixes.
-    if(verbose) qDebug()<<"Marking fixes.";
     markFixes();
 
     if(verbose) qDebug()<<"Restoring visibility.";
@@ -1555,37 +1558,54 @@ void MaskRomTool::markBits(bool full){
     //Same for the lines.
     setLinesVisible(lineswerevisible);
 
-    if(verbose)
-        qDebug()<<"Marked"<<bitcount<<"bits.";
-
-    markingdirty=false;
+    state=STATE_IDLE;
+    return true;
 }
 
 
 
 //Mark up all of the bits where rows and columns collide.
-void MaskRomTool::clearBits(){
+void MaskRomTool::clearBits(bool full){
+    uint64_t count=0;
+    state=STATE_CLEARING;
+
     /* FIXME: This leaves behind some unhandled events.  If calling
      * this from the CLI, be sure to call QApplication.processEvents()
      * to clear them or processing will become progressively slower
      * as the count rises.
+     *
+     * In the GUI, we'll call this with full=false to opportunistically
+     * wipe away bits without hogging the redraw thread.  Like markBits(),
+     * it might take a few frames to finish on large projects.
      */
     foreach (QGraphicsItem* item, bits){
         scene->removeItem(item);
         delete item;
+        bitcount--;
+        if(!full)
+            //For partial work, we need to remove the items.
+            bits.removeOne(item);
+        if(!full && count++>10000)
+            //We'll finish this off later.
+            return;
     }
+
+    //For a full erase, we eliminate items in bulk.
     bits.clear();
     assert(bits.isEmpty());
 
+
     //Reset the markers so we can start again.
     foreach (RomLineItem* line, rows)
         line->marked=false;
     foreach (RomLineItem* line, cols)
         line->marked=false;
 
+    //Next step is to mark the bits.
     bitcount=0;
     markingdirty=true;
     alignmentdirty=true;
+    state=STATE_MARKING;
 }
 
 //Marks the bit fixes.
@@ -1595,13 +1615,16 @@ void MaskRomTool::markFixes(){
      * overlaps a fix than every fix that overlaps a bit.
      */
     bool bitswerevisible=bitsVisible;
+
     setBitsVisible(true);
     foreach (RomBitFix* fix, bitfixes){
         RomBitItem* bit=getBit(fix->pos());
         if(bit) // Apply the fix.
             bit->setFix(fix);
-        else    // Destroy fixes that don't match bits.
+        else if(!markingdirty)
+            // Destroy fixes that don't match bits.
             removeItem(fix);
+
     }
     setBitsVisible(bitswerevisible);
 }
@@ -1621,6 +1644,11 @@ void MaskRomTool::remarkBits(){
 RomBitItem* MaskRomTool::markBitTable(){
     static RomBitItem* firstbit=0;
 
+    //qDebug()<<"Aligning table of"<<bitcount<<"bits.";
+    foreach (RomLineItem* line, cols){
+        assert(line->marked);
+    }
+
     //Make sure all the bits are ready.
     if(alignmentdirty || markingdirty){
         markBits(true);
@@ -1633,6 +1661,7 @@ RomBitItem* MaskRomTool::markBitTable(){
     if(!firstbit)
         alignmentdirty=true;
 
+    //qDebug()<<"Updating counts.";
     //If we have a bit, update the counts.
     rowcount=colcount=0;
     RomBitItem* bit=firstbit;
@@ -1646,6 +1675,7 @@ RomBitItem* MaskRomTool::markBitTable(){
         bit=bit->nexttoright;
     }
 
+    state=STATE_IDLE;
     return firstbit;
 }
 
diff --git a/maskromtool.h b/maskromtool.h
index a898368..547d6a4 100644
--- a/maskromtool.h
+++ b/maskromtool.h
@@ -93,12 +93,18 @@ class MaskRomTool : public QMainWindow{
     void setBitsVisible(bool b=true);        //Show or hide the bits.
     void setViolationsVisible(bool b=true);  //Show or hide the DRC violations.
 
+    /* The state of GUI is whether it is marking bits, clearing them,
+     * or aligning them.  This lets us mark bits in the background without
+     * hogging the rendering thread.
+     */
+    enum {STATE_IDLE, STATE_CLEARING, STATE_MARKING} state=STATE_IDLE;
+
     //Marks all of the bit positions, but not their connections.
-    void markBits(bool full=true);
+    bool markBits(bool full=true);
     //Sorts the bits from the left.  Fast if already sorted.
     void sortBits();
     //Clears all bits.  Useful when we want them out of the way for a bit.
-    void clearBits();
+    void clearBits(bool full=true);
     //Re-marks bits at all of the old positions, but new samples.
     void remarkBits();
     //Marks one bit.
diff --git a/romscene.cpp b/romscene.cpp
index a9940bb..2e2e0b0 100644
--- a/romscene.cpp
+++ b/romscene.cpp
@@ -148,11 +148,6 @@ void RomScene::mouseMoveEvent(QGraphicsSceneMouseEvent *mouseEvent){
 
     updateCrosshairs(mouseEvent->buttons()==Qt::LeftButton);
 
-    /* Whenever the mouse moves, we also update the status bar
-     * to show our position and size.
-     */
-    updateStatus();
-
     //here instead of on release so we can have preview
     if(mouseEvent->buttons()==Qt::RightButton){
         QPointF dpos = mouseEvent->scenePos() - presspos;
@@ -160,7 +155,25 @@ void RomScene::mouseMoveEvent(QGraphicsSceneMouseEvent *mouseEvent){
 
         // update because we already moved it
         presspos = scenepos;
+    }else{
+        //Update some of the bits if they aren't finished.
+
+        switch(maskRomTool->state){
+        case MaskRomTool::STATE_MARKING:
+            maskRomTool->markBits(false);
+            break;
+        case MaskRomTool::STATE_CLEARING:
+            maskRomTool->clearBits(false);
+            break;
+        case MaskRomTool::STATE_IDLE:
+            break;
+        }
     }
+
+    /* Whenever the mouse moves, we also update the status bar
+     * to show our position and size.
+     */
+    updateStatus();
 }
 
 void RomScene::setRowAngle(qreal angle){
@@ -264,8 +277,11 @@ void RomScene::mouseReleaseEvent(QGraphicsSceneMouseEvent *mouseEvent){
          * arrangement.  As a workaround, we remark the bits after releasing the
          * button from a moving drag.
          */
-        if(maskRomTool->bitsVisible)
-            maskRomTool->markBits();
+        if(maskRomTool->bitsVisible){
+            //Clear the old bits in the background.
+            //This will continue until redrawing them.
+            maskRomTool->clearBits(false);
+        }
     }
 }