Well, the bike also felt like a bag of crap at those rpms too. Like it just had the *wrong* mixture. By changing so much on my bike at once I think I have opened a can of worms. See, I cleaned and re-oiled my K&N air filter on the weekend too. Maybe I over-oiled it and the bike is running rich. Or maybe not? I've basically changed too many variables at once and probably need to sit back and have a think about it all. But I'm an impatient bastard, which doesn't help.
UPDATE: OK, checked the air filter. Definitely not over-oiled, if anything could do with a touch up in a couple of spots if I was being pedantic. Also checked my spark plugs, just for laughs, and they have a nice healthy colour to them with good electrodes (they are about 40,000km old)
Also I checked a PCIII map for a 2002 VFR (with O2 eliminators) and it was richened up in the cruise area (4-5,000 rpm, <=20% throttle), not leaned out. So I'm not sure if you're right about it being rich by default there.