I purshased a 3.1 short block from a 91 car, which I do not know. The block had aluminum cylinder heads and aluminum oil pan. I did not buy the heads I will use the ones on the 2.8. I have notice that the 3.1 short block piston raise about .015" over the block while the 2.8 is almost flat with the block. I know I will get a very low compression ratio but that is good because I will turbo charge the motor and could go up to 15 pisg of boost. My concern is the .015" over deck, will it hit the cyl heads( I think they will not because of the gasket that will rise the head aprox. .030. If any one has any experience please let me know.
I have another situation that is the front damper. The damper on the 3.1 block has a cam trigger ring eliminating the pulley for air condition that was on the 2.8 damper. I will use the 2.8 damper on the 3.1 motor if their is not any problem ( please let me know). One more thing I had to change was three holes on the timing chain cover that were bigger on the 3.1 so I put a lock insert to reduce the thread size.
I will post any other changes as they come up.

pistons coming over deck Increase compression. That's why they do that. It's like having domed pistons.

as for hiting something in the 2.8 head... couldn't tell you. some of it will depend on what cam is in the new block, and what the total valve travel in your frankenstien monster ends up at.

You would have been better off to take the whole motor.