Clive,
My '28 600EW has a 9-7/8" flywheel, verses the 8-9/16" you would see on a 350EW. It is not unusual to see this skimmed down a 1/16" or more to remove rust. Yes they both use the same taper. The main difference between the 600 and 350 is a substantially heavier rim and use of a keyway on the taper. And though I have not checked, most of the guts look like they would interchange, once the 350EW switched from the tang drive to the pin drive pressure plate. The one exception is I would think the sprockets would be different, as the 600 could pull a lower primary reduction. Some 350s, like the 1930 H3 for colonial markets, used a heavier, larger diameter flywheel which appears from photographs to be the one for the 600 (not validated.)
There are a lot of differences between 350 and the 600, too many to list in one reply.
The trans is basically the same housing, but the mounting is different. The 600 clamped to the duplex frame tubes right from the start, something the 350 did not adopt till 1927. And even then, the frame tube spacing on the 350 remained narrower, so the housing (and clamp) was never identical. Never checked the internal gear ratios, but pretty sure the 600 had a longer main shaft as the primary chain line would be offset more for the larger engine.
Forward of the seat post the 600 was a duplex frame and the 350 a single loop.
What year is your engine? The 600EW frames did change when they adopted saddle tanks.
-Doug