Krammer did you cut out the part of the motor plate where the starter goes? Make sure that the surface where the starter goes is flat. This will give you about 80% coverage of teeth to teeth on flywheel and starter. THis is what I have been running for the last couple of years and no wear problem any more.
As for the car cranking, was the distributor removed from the motor at any time?? It is possible you are 1 tooth off and having this problem. The timing light trick will work if the motor is spinning over fast enough. Cut the fuel system off and remove spark plugs. Unhook all the injectors and have timing light hooked to #1 wire. THis will let you crank over the motor at a quicker speed. Check your timing. If it comes up OK we have a software problem and need to check the base timing chart. You might at this point fine an FI guy and dyno shop and have the car checked out. ON some FI systems you have retard or advance the timing on cranbking to help the motor to start easier. IF you are snapping flywheel bolts and teeth on the flywheel we need to check the crankshaft end play. There may be a machine problem and causing the crank to no stay centered in the block and has worn out one side of the thrust bearing or the other. end play should be about .005" to .015" max. Anything more than this, pull the
oil pan and do a vision check and look for metal in the pan.
This may help get trans out of car easier, jack up back of motor to clear trans mount and easy twist to remove it. If you have the room a engine crane will handle the weight. Sorry have no easy way to install it. I do it the bull way, by hand. This is also my regular job of tranny R&R. Rick L. Lets stay with the clutch setup you have right now and see if we have another problem first. If you have the flywheel off again, cut a couple of threads of the end to make sure there is no contact with block.