I can't wait for Munbug X. I've been working hard with Munbug IX and haven't quite pulled off a completely successful mission, yet. So it sounds like your problem is that the transfer stage doesn't have enough juice to complete the transfer. I've been having the same problem, though I'm getting closer with better launches. This ship is intended to make its entire transfer burn with the transfer stage. During the transfer, you're supposed decouple the command module, flip it around and dock to the lander, then release the now useless transfer stage. If the transfer stage comes up short, you have a few options. 1) You can adjust the staging mid-flight to drop the transfer stage and attempt to complete the transfer burn with the lander. But this will cause a problem when it comes time to land. 2) You can burn out the transfer stage, flip the command module around and extract the lander, then flip back around and complete the burn. It can be done, but it is a bit rough. 3) Flip the command module around while in orbit around Kerbin, and then use it to complete the burn when the transfer stage runs out. This has been the most successful option for me. On my last attempt, I was about 100 dV shy of a complete transfer with my transfer stage. Having attempted option 2 before, I went ahead and flipped the command module while in orbit. Once docked, I made sure that the command module's engine was deactivated (don't want it fighting the transfer stage) and use the "control from here" option on the docking port on the lander to make sure my nav-ball was oriented the right way. Then I ran the transfer stage until it ran out, extracted the lander, re-enabled my engine, did the "control from here" thing on the command module and completed my burn. And there was one unanticipated bonus to flipping the command module while orbiting Kerbin. By shedding the fairings, I got back almost all of the 100 dV I needed for the transfer. I only needed to burn the command module for a couple of seconds to finish the maneuver. It would be a cheese move, but you could probably re-stage to fire the fairings before launch and save a bunch of dV on the way up. So keep at it, man. You can do it, but it takes a bit of work.
