TurdFerguson - If you search you'll find a lot of posts on the flapper, snorkel, PAIR mods. I've made these mods on other bikes I've owned with no ill effects. When I did the same for my 2006 VFR it ran rough especially right off idle. After a week I put it back to stock. Smoothed it right out. No more off idle stumbles.
I also had the insufficient cold idle speed problem. The PO had just upped the rpm's with the idle knob but that made the idle when warm like 1600 rpm. I set the warm idle back to 1200 and adjusted the wax unit setting. As I recall it only took about one turn of the adjusting knob to give a decent cold idle speed. A lot of folks say you never need to, and should never, adust the wax unit. And that's probably true if it was adjusted right initially... YMMV
Good luck