I would lean more towards the clutch issue myself. I have the same tranny and the only times I've ever had shifting issues was when my clutch wasn't fully disengaging. That also explains the change in performance after you've been out driving for a while. A small amount of air in the lines will prove problematic, but it could simply be that an adjustment is in order. You will find countless posts on this forum regarding clutch performance. Assuming you're using the external push-type slave, it can take a fair amount of "fiddling" to get it right and I have the scars to prove it.
427SC, Torch Red / white stripes
427 Windsor Stroker from Southern Automotive
Delicious example of Beauty + Power.