Help with Kerning and Counter in expressions.

If I were trying to build a timer and were stuck with a font that was not suitable, I would set up an expression to offset a single character layer (center justified to make it easy), then offset the next layer using index-1 by a specific distance. Each character would then be added to the timeline. Then I would hide a text layer (turn it off), apply my timer to the hidden text layer, and retrieve the appropriate character from the master timer layer using an expression for a text that looked at the appropriate character number. A couple of sliders to control the horizontal space between layers, and I'd be done. If you used the layer index, you would only have to write two relatively simple expressions, then position the first number in the layer. Something like this would work for spacing the layers:

1. Create your Master Text layer and add an offset value slider.
2. Create a new empty text layer below the Master Text Layer and give it a name like "Char"
3. Add this expression to the "Char" layers. Source Text Property:
   

   srcTxt = thisComp.layer("Master Text");
   chrNo = index - srcTxt.index;
   srcTxt.text.sourceText.slice(chrNo - 1,chrNo)​

4. Duplicate the layer and add this expression to the "Char" layer's Position Property (it should now be on the bottom of the layer stack:
   

   ldr = thisComp.layer(index - 1);
   hGap = thisComp.layer("Master Text").effect("Gap")("Slider");
   x = ldr.position[0] + hGap;
   y = ldr.position[1];
   [x, y]​

5. Duplicate the "Char" layer until you have enough copies of the layer with both expressions under the "Master Text" layer to use up all the spaces.

You have now created a pseudo monospaced font from any font. 

You can turn off the Master Text layer or make it a guide layer so it will not render, and you've got a nice stack of characters that can be positioned and adjusted anywhere you want by just moving the first layer (Layer 2 in the screenshot).  Apply your own counter, and you've tot it. 

EDIT: While Dan was solving your problem, I was writing my post with the expressions. I have used this kind of stacking layer trick before to fix font problems. 

I downloaded your 7-segment font from dafont and it comes with a mono-spaced version (Digital-7 Mono), which I think will solve your problem.

I have not looked at your AEP yet, but kerning problems are solved by choosing a Monospaced font. Courier is one example. If you use anything but a Monospaced font, the width of each character can be different. If I get some time later, I'll look at the project.