I have a 91 300zxtt and getting ready to buy a new mother I have found that engines that were auto are cheaper then a 5 speed why is this is there a difference in the engine

The auto had a tiny bit less power, I believe the cams were to blame, you can swap over your TT cams, also the engine backing plate and dont forget you have to remove the flexplate adapter and add a pilot bearing. My advice is to stay away from pallet motors and fix whatever is wrong with yours, unless the block is ruined it can likely be rebuilt for about as much an an unknown mileage unknown condition pallet motor.