i always thought what you described is a synchro issue, though sounds like you've done more with gearboxes than i have.

you have no power at 3500rpm? i always found in rally that holding third gear as much as possible is much faster than down-shifting to second. though second often results in wheel spin in dirt, you are essentially eliminating two gear shifts (down to second and back up again)

it's off topic but surely you can have an engine setup with power lower than 3500rpm, my pet hate is spectating rallies, too many cars running twin webers/dellortoes bogging down in the corners as they have zero power at low revs (go the SU's!)