Not knowing exactly what you are building I cant really visualize. I had thought of using a 3speed as a jackshaft to a 3speed rear wheel. Never ran gearing to see if the reductions were in the needed ranges, but gut says probably.
Think of the combinations of gears two 3sp IGHs would give! This would also leave the pedal system totally alone.
Thoughts after putting as many miles on the bike as the weather will allow is that its really a GREAT ride. Have got the shifting worked out to where it very pleasant to ride. When shifting down it works exactly as an M/C you just need to match the engines speed for the lower gear. When shifting stopped its best to roll the bike slightly to catch the shifted to gear, the clutch has to lock in place. Otherwise it will engage under load on take off. This is avoided if the gear selection is done while just rolling to a stop.
Riding this thing reminds me of when I learned to ride a Harley 165 as a kid. Has the same sound basically and seems about the same on power to weight ratio. I loved the old 165, glad this bike reminds me of it.
I may have gone strong on the gearing, The overall ratio with the mismatched sprockets on the hub is the same as a 30t sprocket even though its a 32t. Low is a bit high. Fine for the flats here but lower overall gearing would be in order in hill country, IF you are planning on starting from still. Not a problem pedaling. Other side of that is its nicely relaxed at a mid 30s cruise. With it current gearing the calc. says it would have a 44mph top end @7K rpms, which is not really wound out compared to a single speed(9K+). Stock engine probably wont pull the wind loading at 44, but sure makes the 30s nice!