hi Terry, the easy part here is the starter hooks up the same way on an auto as it did on the manual. I am sure you have the fly wheel correct because if it were backwards it would rub on the block and/or the alignment with the torque convertor would be off.
The most likely problem is the starter itself being the wrong one now that it is a auto trany. They are different from the one for a manual trany.
You can try shimming it to get a proper fit or purchase one made for the engine you have (4 or 6 cyl.) and the model trany you installed.
Hi, which motor do you have?
If its the 6 cyl. the starter bolts directly to the bell housing and there should be a plate that is the same size as the bell housing that is sandwiched between the block and the bell housing. I do not think the manual trany has the convertor drive plate so make sure you have it installed. If the plate is in place and the flywheel is in place there is no other conditions that can cause this other then having the wrong flywheel.
If you have the 4 cyl. the starter bolts to the block and there are shims that go between the starter and the block to position it correctly. Again other then that there is no other conditions other then the flywheel that can cause this problem.