I'm helping a buddy out with his car and he had to swap his motor (mazda 6 sorry not lexus) he had difficulty putting the trans back on the motor but we finally got it to thread and get pretty close. The problem is he has about a 1-2 mm gap around the bell housing and block.

Like a dummy he put the motor in the car and was hoping that after in the car it would wiggle into place...

Its an auto v6. What do you guys think?

 

The transmission should slide all the way down. If it doesn't, something is way off. I think the flex plate or torque converter is installed wrong.

 

Can you spin the torque converter?? With the trans mounted to the engine?? If not then the torque converter isn't sitting all the way in the trans.