No you don't want to try that it that it would be a bad idea! If the convertor is not fully seated into the front pump correctly there is a chance it will ruin the front pump. When it's seated correctly the convertor will be loose enough to have a gap between it and the flex plate and will be able to side up easily to the flex plate it should have at least a 1/4 inch gap between the convertor stud seats or flats and flex plate when the convertor is bottomed out in the front pump. If it's tight against the flex plate do not run it or drive it until you pull it back apart and get the convertor seated into the pump correctly. Good luck 
Try taking all the torque convertor nuts off and see if it will move back into the pump any and have the gap as explained above. That will tell you if the convertor hub is lining up going into the front pump and input shaft correctly. When they slide in and bottom out there is a solid thunk like sound after awhile of installing them it's much easier and you know that it's right. After rereading your first post this morning like you stated I am also wondering about the new flex plate, with it setting on a flat surface did it match up to your old one in height? If it's not the same height (measures less) then it may be pulling the torque convertor forward enough to cause the studs to hit. Did you get the rockers to now oil good? Good luck
Ok did you change the oil and filter yet so there's no shaved metal in the engine. What compression did you make the engine? Good luck
it Sounds pretty heathy!
You were much closer on the C.R. I ran these numbers .030 over Bore 3.710, stroke 3.126. 48 CC chamber, .050 compressed head gasket, flat top piston, .015 down the hole I guessed at that spec since you did not mention it so that may need some adjusting but that Equals a 10.3 compression ratio. Stock dished piston deck height is .019 down the hole that would drop the compression down some to 10.19 to know for sure you would also need the piston pin height. Yeah my hearing is not the best at some tones I did hear it the second time. Have you done any plug reading yet? You might want to make sure that it's a little on the rich side tell you get everything dialed in.
seems like you should be close on C.R. For 91 Oct. fuel. You could maybe try a water / alcohol mix injection unit for racing or higher RPM. Have you set up the curve on the distributor yet? If you need to run that much base timing you would need to limit the total advance too. Good luck
