'73 500, stacks, Supertrapp with the baffle removed. Stock needle one clip from the bottom. Stock slow jets. Mains drilled to 130. Your airscrews are WAY too far out, IMO. Mine were at 1/2 from closed with the baffle in the pipe, now fully closed and idling slightly lean, with the baffle out. For you to be running stacks, aftermarket pipes, and barely-richer-than-stock mains, something is effed up if you're two turns out and still rich.
ADJUST THE FLOAT HEIGHT! I've never played with one of these bikes that didn't have the floats way out -- and you will get nowhere but the loony bin trying to jet a bike with wonky float heights.
Then, IMO, you need to run some WOT plug chops on clean plugs -- and, also IMO, first gear chops won't cut it. The thing only does 100 MPH in top -- I'd find a freeway or something and have at it.
BTW -- I rarely dick with the needle position. That's just moving the "map" up and down, and is fine tuning: something to do after the fueling is 95% sorted.
Bottom line: You tried a free flowing exhaust and a relatively free-flowing filtration set-up with stock carb settings and got... rich. Which means something's screwed up. My guess is float heights. If that's not the trouble, it may be worth checking ACTUAL jet ID. Just because it SAYS 100 doesn't mean somebody with a drill bit didn't get there first. And as for the 109's that you drilled? Are you sure they're actually 109? If you made a mistake in bit selection, or if you used a power drill and a few passes "just to be sure", you may have 1??s. (No offense, I hope. Just trying to toss out idears.)