I did a little more research on the issue yesterday, and also rode my brother's 2004 classic with about 3000 miles on it for comparison. It accelerates OK up to about 45-50mph, then if I keep running it at 45-50 or thereabout it seems to surge a bit - seems to gain and lose power. It definitely runs smoother accelerating or decellerating than to keep it at a constant speed. My brother's bike seemed substantially smoother at those same speeds. It's mostly 4th gear that I notice it going 40-45 or 5th gear going 50-55. I changed the plug and re-checked the valves.
How about this one... His petcock, when turned on, dribbles fuel out, when turned off, dribbles fuel out a bit slower. My guess is that it is fuel-starved due to a screwed up petcock.
I did my 300 mile tune up last week myself. My bike ran very rough for the break in period I kept it under 45mph. Too the point it would cause my hands and seat to get numb. I put in Mobil 1 Synthetic 20W50 the difference was instantly noticeable, the bike has smoothed out quite a bit and is now a joy at any speed, I believe the new lube did the trick. This might not be your problem but it is worth mentioning, I initially balked at paying $8 a quart for the Mobil 1 but figured what the hell, and am glad I did.