is there a diff between at and mt
 

i am rebuilding a 13b and i asked his guy about port and polish and he asked if my motor was from a at or mt and my engine is from a at but i am puting it on a mt so dose any one no what te diff is between the mt and at on the motor

The counter weights. If you are putting the AT engine into the MT car you will need a light flywheel using the AT weight in the rear or swap front c-weight from the MT and use the stock flywheel from the same year.

U can remove the flex plate and counter weight from the engine and replace it with the stock flywheel and clutch setup and be fine. It's really not nessessary to go with light weight flywheel unless u just want to.

I suggested not porting the last motor I built because it was going on an AT car. The AT is terrible until 4000 RPMs, so I didn't want to hurt the low end torque any more.

That's probably why he asked when you mentioned porting.

also, does the eccentric shaft in the AT carry a pilot bearing?

It must be the same shaft for all the 5spd ---> auto conversions that have been done, but good point!