the HF engine harness will not work in the Si car - ususally you will get a Check Engine Light and code 15, because the HF has the igniter wire running thru the connection on the driver's side and the Si has the igniter wire on the passenger side (there are other differences, depending on the year) - that said, it sounds to me like you don't have the 88 Si chassis harness or that someone has rewired it - the HF engine harnesses will not plug into the 88 Si harness, as the 88 Si had a square 6 wire connector at the driver's side shock tower - the 89-91 Si and 88-91 HF all used a round 8 wire connector
this is the 88 Si connector