high pitch squeak when engine bogs?

[budomove]

With an hf tranny now installed in my d15b1 civic (thanks to Ben), I have been hearing a new sound. First of all, the engine bogs and threatens to buck before the car warms up just after upshifts. It only happens after upshifts, as if I am upshifting into too high a gear. It now happens sometimes after the car warms up, and it is in all gears 2-5 for a short duration after upshifts. With the clutch depressed, the sound goes away, and although that might in some cases hint at the input bearing, I think in this case it is just the mismatched low torque engine/tall geared tranny, any thoughts? The sound is a high pitch squeak that pulses and sounds as if it is a circular motion that is causing it, which again may hint at the input bearing, no? Please Help!

EDIT: Ben, we didn't change ignition timing, cuz we couldn't budge the distributer, right?