I am presently doing the LS crank, LS rods and pR3 pistons in a b18c1 block but when assembled the piston is above the block deck to a point where the top ring pistons come out ATDC.

I have read that many have done this swap before: what am i doing wrong

 

Wow, theres no way you have the right parts if thats happening.

 

sounds like you got rods that are too long to me.