P0335 question

Finally had a chance to get the car out for another shakedown cruise yesterday and ran into a little trouble. I now have a check engine light showing "P0335 No Crankshaft Reference Signal at EFI ECU". Which seems strange to me since the car runs and it doesn't seem like it should at all if it doesn't know where the crank is.

A little background info:
car is a 91 stealth TT
ECU is a 98 or 99 SL ecu, with a custom built blackstealth boomslang, running Chrome (I'm not using it for boost control/display obviously).
Engine is set up like a 91, no crank position sensor/trigger, just the adjustable CAS on the end of the read intake cam.

Car ran ok for about 25 minutes, up until I stalled it at a light. After that it refused to start for about 5 minutes. Then it started up no problem and ran the same on the 25 minutes home as it did on the way out. But, when it restarted at the light the check engine light came on and stayed on for the ride home.

Does anyone have any ideas? Do I just reset it and swap out my CAS for another (I'm pretty sure I have another used one around here somewhere...) Should my car have run at all with a bad CAS seeing as thats its only way of knowing where the crank is?

Additional details:

I did recently have my less than 5,000 mile old timing tensioner fail completely. I've no idea how many teeth were jumped, the belt was loose enough that I couldn't turn it back to TDC by hand without the belt jumping. So I cut the belt, pulled the cams, then replaced the timing components.

As part of this, there's then the potential that I either A) flipped the CAS blade 180 degrees when I reinstalled (although I could have sworn I double checked that) or B) screwed up the wiring harness... maybe a broken or partially broken wire conductor at the CAS connector? I don't know what "A" would result in and the connector "looks" ok, though that doesn't mean much.

I seem to have lucked out on the valves. I didn't seen any loose rockers or valves that weren't returning to full closed, and the compression test on the front bank looks good, and that's the one the timing belt was loosest at.

Once it sets the code, the lamp stays lit until you clear it... It only has to see the problem for 4 seconds to set the code. Sounds like whatever made it die and not restart right away is probably your issue. could be a bad CAS, could be a wiring issue.