If I have made a stupid mistake, please don't beat around the bush... just tell me so I can fix it!

Background:
LH 3.1 92 245 resto-mod project.
Manual trans to auto conversion (no, this isn't stupid... there are reasons....)

Symptoms:
The engine will run but only with a healthy amount of throttle, it will not idle.
It backfires out the exhaust badly.
The Injection and Ignition computers return the "all is fine 1-1-1" code.

Tests to date:
Verified the following timing marks:
Crank to cam
Crank to intermediate shaft
Crank to distributer
Verified plug wire order 1342, all is good
Timing light (with engine kinda running) finds the crank timing mark a good 45 degrees off of the 0 degree TDC mark on the timing belt cover. Amazing it even runs.

Theory:
When I installed the flex plate on the rear of the crank, I aligned the double wide hole on the tone ring with the location of the tone ring sensor (just behind the head at the top of the engine).

Did I install the flex plate/flywheel at the wrong angle? If not, then I will run an electrical check on the tone ring sensor. Why am I getting the idea that the engine or trans is going to have to be pulled out again? Perhaps I'm a pesimist!

Any help will be greatly appreciated!

Thanks,
Jorrell