First, let me say: awesome! The increase in power is enough alone to make me want to headbang into a brick wall (figuratively speaking).
I was wondering though what you mean by "The drums don't sound right". Are you talking dynamics, the mix ect.?
What I hear, when the drums come in, is a very thin, centered sound. The snare as well, has a very thin, almost midi like quality to it.
I want to compare it to the double/bass and snare timbre in Animals as Leaders:
The bass drum is heavy and works as a powerhouse with the bass guitar. Also, the snare is more to the forefront, and, though it is crisp, it has... resonance! Rather than, "Ta" for a hit, it kind of has a "Ta -ah" aura, or a tapering of sorts.
I'm probably talking out my aftend, and you know a HECK OF A LOT MORE about writing prog metal than me, but that's what I hear. I think it goes back to your samples.
If you found yourself a real powerful set of Bass Drum samples, it would help fill in some of the bottom that I believe the piece is lacking.