Matt.....thank you! That sounds exactly like what I did. When I pulled it all apart I found every single motor plate bolt backed out, oil leaking everywhere, and the 3/8" shouldered bolts (with Nylock nuts) had come loose enough that the plates and gears were moving! I think the first failure was a forward trans plate bolt into the #1 coupling gear.
I've got the rear engine about ready to go back in, with a standard primary cover and a Barnett clutch. The damage was contained to the front two coupling gears and the forward crank gear. I've already added tubes and mounts to the frame (ditched the motor plate), converted back to stock oil system, found my internal water leak, and got my friend started on the case plug to fill the hole I'd made for the #3 coupling gear. I'm hoping to have it running late tomorrow; plan to run APS-PG-750 if it doesn't break again. If it breaks, I have my freshly built 500cc engine ready to plug in, which would run against my own record.
Even before reading your post, I was thinking that pairing them as a V4, with pistons moving together, will be the best plan. I'm pretty sure the right-side engine can have it's crank installed backwards, putting the drive splines facing. I'll make a cushioned coupler (similar to a boat outdrive piece) and take the drive via belt to a Harley clutch and transmission. I'll probably put the intakes in the exhaust side, on the right engine, just as Honda did when they used the 500cc engine for a flat-tracker. It'll be easier to bend exhaust around, between the engines, than bend carbs.
All I need now is a winning lottery ticket....JimL