I disagree with your statement about them not playing well together. Their first season together they had 50 wins and pushed a far deeper team (Mavs) to seven games in the playoffs. The only reason they lost is because Yao was in foul trouble and they didn't have a power forward capable of stopping Dirk.
Now that Yao has emerged as The dominating Big Man in the NBA and T-mac has had a whole season to heal is his back, not to mention they acquired a more traditional point guard in Rafer, a defensive specialist in Shane Battier, an athletic shooting guard in Kirk Snyder and a three point threat in Steve Novak, and Luther Head. The rockets are primed for Deep Postseason run if not the Championship. They have all the tools the Miami Heat had during their championship except Yao is younger and can hit free throws and will not be limited to 5 point games as Shaq was.
Another thing, if James Posey and Antoine Walker can shut down Dirk, I am pretty sure Shane Battier won't have much of a problem.
Dirk= a soft pu$$y who will choke in the clutch