That's so we'll explained, thankyou.Your jet sizes are pretty much spot on for your mods. I have similar mods and pretty much the same jetting. A couple minor things though - 3 turns out on the mix screws is quite a lot, especially with you being 2 up on the pilots. Did you set the mix screws for best running, for fastest, smoothest idle speed? Also, I'm only one up on my pilots, but that may be because I did some porting clean-up when I rebuilt it. Before the rebuild, I was 2 up on the pilots too. I had read that better flow can require smaller jets because it pulls more fuel through them. Well, it seems that happened to me with the pilots anyway. The mains were fine and stayed at 140. The other thing I'll mention is that it's rather odd you can run the needles in the stock #3 slot with the bigger mains. On this carb set, usually any increase in main jet size, even one, requires you lean the needles a step to cure upper midrange break-up under heavy throttle applications. Now, normally you probably don't ride the bike like this, but these CV carbs are rather forgiving and will mask over minor jetting glitches unless you push them hard.
So, here's the upper midrange to main transition test, to see if your larger mains are making the upper midrange too rich - in 2nd or 3rd gear, starting at around 3K RPMs, roll the throttle full open and run the bike up to 5 or 5.5K, through the upper midrange and onto the mains. Watch for any stumbling or break-up between, say, 4 and 5K. If you get some, you need to lean the needle a step. But now you said you had it like that but it made the midrange sort of "flat". Well, you may be able to lean the needle a half step using a washer. That could be enough to fix the stumbling but not have such an adverse effect on the rest of the midrange.
Let's talk about the mix screws some more. The factory set point for this carb set is 2.25 turns out but usually they like a bit more, like 2.5 or 2 5/8 turns out. But larger pilots often make them dial in best at less turns out, sometimes as low as 2. Luckily on this set, you can hear the effects your adjusting is having. It does help if you turn the idle speed down a little, to around 1000. You'll be able to hear the changes better. What you're trying to find is what we call the "sweet spot", a range of about 3/8 to 1/2 turn where the engine idles fastest and smoothest. I start with the screw at the factory spec then pick a direction, in or out, and start adjusting it 1/4 turn at a time. Usually within a turn or so from that factory setting, the idle speed will begin to falter and drop off, and the cylinder will begin running rougher. Note the turns at that point and start going in the other direction until the same thing happens. This should allow you to find the "sweet spot" range. I like to set the screw at the rich end of the range (screw more open), as rich as I can get it before the speed drops off and rougher running sets in. I think this helps alleviate popping on decel.
Yes I haven't retuned the pilots since I've resynced the carbs, I'll check that but that's where it liked it beforehand. I definitely thought it was odd too, especially when I was around 2 turns out on a size smaller pilot jet (which is even weirder cause I thought a smaller would require more turns out) so maybe I should go back. Wonder if the jets are stamped wrong, will have to measure.
And I'll try doing that test, though I don't recall feeling any stumbling consistently around 3.5-5k rpm, it might do it occasionally so I'll try a washer and see how it feels. Preferably a thin as possible one yeah?
It does seem to flatten out above 5.5k, though looking at dyno charts it seems the motor flatlines around those rpms anyways.