Just use the 86 valve cover.
They modified the EFI and moved it around the two EFIs are not compatable.
The wiring and EFI are different, but the block and head are pretty much the same.
If you use the 96 EFI just make sure you use everything including wiring, computer, and all the junk under the dash.
Just seems like a lot of work to upgrade the EFI to 96 if the 86 EFI works fine.