I'd say you're on the right track. You shouldn't worry about harmonics, as you aren't connecting the cranks together 100% rigid, as a single piece crankshaft would be. The harmful high frequency vibrations won't transfer between engines.
For the phasing, 45 degrees is right, but it's not because its a 90 degree engine. That's just the angle between the left and right banks of cylinders. Since a 4 stroke engine requires the piston to go down and up twice for a complete 4 cycles, that's 720 degrees of crankshaft rotation for each ignition event. Divide that by 8, and you have a cylinder firing every 90 degrees of crankshaft rotation. Split that, and you get 45 degrees of phasing between engine 1 and 2.
Now, for that V-16 sound, and other considerations. I don't know any V-8 firing orders by heart except a Chevy, so I'll use that as an example. They go 1-8-4-3-6-5-7-2. If you just take engine number 1, and put it at straight up TDC, then put engine number two 45 degrees after it, you'd get 11-88-44-33-66-55-77-22. You get two exhaust pulses on the left, then two on the right, two right again, two left, aaahh it looks like this: 2L, 2R, 2R, 2L, 2R, 2L, 2L, 2R
See the issue? There's a point where you'd get 4 in a row from the right, and nothing from the left, and same later on the other side. That won't make for a good exhaust system, but it might sound interesting.
So, you'll probably want to go something like 135 degrees out of phase.
Let's see;
engine 1 L-R-R-L-R-L-L-R
engine 2 -R-L-R-R-L-R-L-L
Yup, that does it. There's no more than two lefts or rights in a row.
Putting numbers on that:
1-8-4-3-6-5-7-2
-2-1-8-4-3-6-5-7
So your engine number two fires cylinder 1, 45 degrees
after engine number one fires cylinder number 8.
Then you hear LRRLRRLRRLLRLLRL right?
Too bad I figured all of this for a Chevy!
As for the coupling of the two engines, I would be inclined to use a short driveshaft between them. They're relatively inexpensive, and you wouldn't have to build your engine mounts with a micrometer. If you use a coupler that doesn't allow for enough end play or side shift, you'll be taking out bearings I'm sure, if not cracking a crankshaft. Plus, I expect that you'd have to mount the engines solid, even the engine torque twisting the frame would, well, I'll just stop.
One of my driveshafts on my 8literbeater build is only 7.5 inches long, and one could be made even shorter.
I hope that helps. I have never actually done it before, but I've built many highly successful projects in my mind!
