It sounds like something fundamental has been over looked here. In this case I would always recommend going back to basics and re-checking everything. I would recommend, (in this order):
1. Carry out an output test on both ignition and injector outputs and ensure that IGN1 and INJ1 are operating correctly on Cylinder 1 and that IGN2 and INJ2 are opperating on Cylinder 2.
2. Remove the spark plugs and the cam cover, turn the engine over until the sync tooth just passes the sync sensor. The next tooth on the crank sensor is your "Index tooth", continue rotating the engine until this tooth is in line with the crank sensor. Now rotate the engine until you reach TDC #1 (compression) and measure the number of degrees of crankshaft rotation this takes. Use this number as your CRIP (you can check and adjust this later with a timing light).
3. With the engine still at TDC #1 make a paint mark on the cam drive pulley which you can line up with a reference point somewhere and mark it so that you can identify it as #1.
4. Now turn the engine until culinder 2 is at TDC (compression). I would expect this to be 180 degrees later but it could also be 540. With Cylinder 2 at TDC make another mark on your cam drive pulley so that you can identify it as #2.
5. Connect a timing light and spark plug to Coil #1 and crank the engine (without the plugs installed). You should be able to see your #1 TDC marker on the cam pulley line up with the timing light.
6. Now connect the timing light and spark plug to Coil #2 and crank the engine. You should be able to see your #2 TDC marker on the cam pulley line up with the timing light. If it doesn't line up you need to correct the value in the Odd Fire TDC setup.
7. Re-assemble the engine and run it to re-check the CRIP with the timing light.
8. Check for any diagnostic errors.
I have also noticed in your file that you have the Dwell set to 1. This is un-likely to be correct. Check the coil primary resistance, if it is very low (around 0.3 Ohms) it may be that you have CDI coils that are not suitable for use with the Bosch module. If it is higher (say 0.8 ohms or higher) they should work ok but I would expect you would need a dwell of at least 1.8. You would need to have the coils characterized to get the correct setting.
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