Wow, man, you have alot of work ahead of you!
But don't worry, it's perfectly feasible! Honestly, I think you did the hard part - shooting it! Now is the easy part, it's just you and your computer!
Before I get into any specific answers, may I recommend that you read one book? This one: The DV Rebel's guidehttp://www.amazon.com/dp/0321413644?tag ... 8QWSWK3X5&
It will answer so many questions for you! It's honestly the best book ever written for making movies on a desktop computer that are intended to be shown on film in a theater. After reading it, you will have a final Master fileset that you will use to make the film print or any compressed version you want. Seriously, check out the book. The book deals mostly in After Effects, though. Most of the techniques will cross over fine, however, as long as you know Combustion a little.
First, your tracking... Boujou and Matchmover should both be able to handle your footage just fine, although I've only dabbled in Boujou. My tracker of choice is Syntheyes. But you should be fine with what you have. Don't know if you saw this, but Zach made a tutorial about using Boujou.viewtopic.php?f=31&t=3616
Honestly, the only person I think I've ever seen get good results from the 3dsMax built-in tracker is Tyson, who runs these forums, and he's a bit of a genius/prodigy, so his results aren't the typical user's experiences. Are you using the auto-track features of your tracking programs? Because that doesn't solve everything. If that's failing, you'll definitely have to really learn how to use the manual features, how to track things individually, and then create the track from that. But those programs are definitely capable of handling whatever footage you put into it. If your shots are fixed shots, you may not need to track them at all, though. Just set up the environment in Max. You mention the lens doesn't seem right - could it be lens distortion? hard to tell without some screenshots. But those tracking programs are perfectly capable of measuring the lens distortion, and Combustion should have a lens distortion effect/filter that you could use as well. Some people take the lens distortion out of the footage, composite, then put it back in. Other people just set up a camera that matches in Max.
Have you seen the one and only book on tracking? It deals with both programs you are using, so it should apply perfectly to you. Awesome book!http://www.amazon.com/Matchmoving-Invis ... 0782144039
Unfortunately, I can't give much guidance on the use of Combustion. I haven't touched it since version 3.1. I was using it to pull keys fro "Starsky & Hutch", and just after that, After Effects started including Keylight keyer, which quickly became my favorite. Combustion should be able to handle Log and Lin and any color space you want to work in.
I've made a couple short movies now, but all my work was done through After Effects. Don't be insecure about the programs you've chosen! They are all great programs that can do exactly what you want them to do. It just may be tricky getting to that stage. I only use After Effects because that's the program I learned first, I'm most comfortable in it, and thus, it's become my favorite. Here's a thread where you can see my progress on my last short movie, if you want.viewforum.php?f=38
For more specific help, you'd have to start posting screenshots and/or sample moves. It's very hard to judge what's wrong with your track without seeing a preview of your character in the shot and seeing how it's tracked in. There was one shot in my short where I wanted 3d missiles flying overhead. The shot is a completely handheld, free moving shot. I didn't even bother to 3d track it. I set up a virtual recreation of the scene in Max by just guessing distances, I didn't measure anything on set. I rendered the missiles out from that perspective and tracked them in After Effects, all 2d. I didn't even render smoke from 3d, just made it in 2d. Here's a screenshot where you can see my Max scene, and the view through the virtual camera.
I know this wouldn't work for integrating a 3d character into a scene, but, depending on the shot, sometimes it can be effective to just recreate the scene by eye. Check out that tutorial on Boujou that Zach made. Hopefully that can get you going.
Keep posting though, there's a bunch of smart people here, people who use all the programs you use.
And congrats on shooting your short! That's the really hard part!