Hi Jeff -
I replaced my W-C toilet with a compact Jabsco. I knew that the bolt holes (actually lag screws - not bolts) would never line up. So, I bought a large white plastic food cutting board from a restaurant supplier in Toronto ($18.00). I fooled around with the new toilet, trying different placements. In the end, I placed it a slight angle thus creating more "legroom" for sitting. Knowing where it was going to end up, I trimmed/cut the cutting board such that it covered the old holes in the floor. The floor is fibreglass with plywood under it. I put a few blobs of 3M4200 on the underside of the trimmed cutting board and Robertson screwed the cutting board, exactly where I wanted it, to the floor.
I, then, was able to lag screw the new toilet to the new "floor", going through the cutting board AND the old floor. I had to buy 4 somewhat longer lag screws as I was going through more material (and attaching the toilet even more solidly than it was previously i.e. through a thicker floor).
I pre-drilled starter holes for the both the Robertson screws in BOTH floors (after placing and "glueing"down the cutting board). Then, I pre-drilled starter holes for the 4 lag screws for the toilet. It is VERY solidly attached.
Other suggestions - If you are changing the holding tank, excellent. If you are doing that, make certain that you change ALL the hoses. Break the bank and buy Raritan top-of-the-line hoses - they retard any smells.
Just think .... a nice new toilet plunbed into a nice clean tank using nice clean hoses. Priceless.
I've attached a photo of my installation. The Jabsco does a fine job.
Ernie A. in Toronto