Don't sweat it, it'll work just fine as it is. I have the same van ('93) and our bikes (RM's) fit just fine. The left side of the van will be a little tighter for vertical room than the right, but it'll work anyways.
If you still have the the stock rear bench seat brackets, they will be little bumps, but we've left ours in w/o trouble.
I have mine set up to hold two bikes with a home-brewed front tire stop bracket, which couples into the bench seat brackets.
BTW, We really like the van. It has worked out very well, and I'd have a tough time going back to a pickup again. Also, the Ford vans seem to run forever. Ours has 218k and most of them at the races have even higher miles.
Good luck with it!