Mostly stock S4 Tii, I followed Aaron's MS2 guide as closely as I could, aside from some microsquirt-required deviations.
-All GM Sensors, including TPS.
-Throttle-Body Mod
-Stock IAC
-Stock Coils
-Stock CAS
-MicroSquirt 3

I finally got to the stage of firing up on microsquirt on my FC Tii. I warmed it up, got it to the point where it could 'idle' and then went to zero the CAS. I set the timing to fixed @ -5*, and to my surprise I could not adjust the CAS far enough to zero at the Leading mark. I pulled the CAS and reinstalled it a few times as per procedure, and it yielded the same result. I found that in order to get a proper null I had to index the CAS drive over 2 teeth from the normal position. At first I thought there was something wrong with my timing light, but that would be unlikely. What the hell is going on here? I triple checked my trigger settings and they definitely match what Aaron used in his guide on MS2. It's running pretty well, so I'm not sure whether this is a problem or not, however...

I drove around a bit to touch up the fuel table, and I found that at about 5000 RPM, I lose sync briefly, and the fuel relay cuts out for a fraction of a second. This might be unrelated to the previous issue, but It's worth mentioning. I have the squirt grounded to the rear rotor housing, and the shielded CAS cable grounded to a ground bus at the squirt. I still need to try closing up the tooth gap in the CAS, how close do I want this?

One more question: In Aaron's writeup, his final bin for the WUE table is set for 110%. Is there a specific reason for this? I set it to 100% as I don't like seeing the WUE Active light on all the time in TunerStudio.

I can post an msq and a log tonight when I get home from work, and I haven't tried logging the CAS trigger yet, but I will.

 

Here's the msq...
Record 5618 on the msl shows a good example of the sync loss.

 

So I've reduced the length of unshielded wires at the CAS end of the cable, and closed up the VR gaps. That seems to have improved the situation, at least in neutral in the driveway, it does not lose sync - need to take it for a drive still. I double checked all my wiring and tried using falling edge triggering in all other combinations, but it won't run that way. Still have to have the CAS stabbed two teeth out on the drive gear. I changed the first trigger to 5* and I'm able to get the timing zero bang on that way.

 

I wouldn't worry too much about the CAS being stabbed two teeth off as long as you have it in a position where the timing light confirms the expected timing set in the MS, in this case the 5* aTDC set for the leading timing mark. For a while, there were multiple write-ups that had the CAS stabbed at different places, and some other changes in the trigger wheel settings between them to account for the difference. To be perfectly honest, I don't remember which method I settled on since I take a picture of the CAS with the back cover off before removing it each time so I can get it timed the same way when re-installing.

Edit: To add to this, these engines (with stock ports) will idle over a very wide range of spark timings, at least 40* bTDC to 10* aTDC, so just the fact that it idles doesn't really tell you much - its set so late typically to get the MAP up because late timing is less efficient, so you need more fuel and thus more air to keep it idling, which helps with stability since higher intake pressure gives less internal exhaust gas residuals. This also gives you more control over the idle with just the spark timing, so the engine controller can respond more quickly to keep the idle stable as you turn on accessories, lights etc.