Welcome aboard Rick!
Congrats on the MT, it is a machine that can make very impressive recordings.
I am not sure there are easy answers to your questions. Spend some time getting familiar with this site and the threads. You will find many interesting threads under recording on the MT and under the mics section too.
There are threads that help with which CF media cards to buy. Generally the older slower cards work better, but M-Audio recently did another firmware update which partially was to help more media be sucessfully matched. You should make sure you have the latest firmware.
As for line in, mic in, what you really have is Low Med High, with differennt impedances. Also using the 1/4 inch TRS jacks are much leass sensitive than the 1/8 jack. There are some really useful links posted in different threads too. Look for the Guysonic (Sonic Studios) link and that will take you to some really useful statistics on the MT (Guy are you out there??).
A battery box works really well with most mics although you do also have phantom power available. A lot depends on how you use the MT. Also there are battery boxes that fit right on top of the MT or standalones too. Much may depend on whether your recordings will be done in open settings or not.
There are so many mics that work well with the MT. Again if size is a factor or if it is not will make a big difference on recommendations. Budget too.
That is what I have off the top of my head. Others with better memory's than I will help with links a recommendations too. Again, every questions and thought you will have has been covered in the links below, and there is a great wealth of info to absorb. That should help with many of your questions, and we are here for the rest of them too
Have fun....
Edit: Here is the Sonic Studios link, with what I feel is a great deal of useful information:
http://www.sonicstudios.com/mt2496rv.htm