I agree with your description that it feels like 5 cylinders til 3000rpm and then 6 cylinders thereafter. Try upping your base timing, that way you can get more power from your 5 cylinders until the 6th one kicks in.
Running a base timing of 7.5 degrees has made this problem a bit more tolerable.
With regards to a new engine, I don't have the time/money to do a fresh build up, so I hope it doesn't take a new engine to solve this problem As far as compression is concerned, the last time I checked (mid last summer) my compression was fine. If my memory serves me correctly I believe all six cylinders were between 149-153psi. I'm planning on checking it again sometime in the next few weeks and I'll post numbers at that time.
Oh yeah by the way, I took a look at my TPS voltages and there was a smooth transition from closed to WOT. So I guess that rules out TPS.
