Im far from an expert but I can tell you that I started the same way you are.....
first was my stock 3906 maxx new out of the box with 6cell stick packs
then I got EG4600 7 cell nimh packs and was super excited about the performance compaired to 14.4v
then went 2 700ho kit from kershaw....even more power but rough on the esc it killed 2 of them
then I got the new 3905 and did the V-twin brushless with 2 VXL systems for a while on a pair of true rc 6400 2s2p lipos......the truck was sick..heres a video of it on 2s
http://www.youtube.com/watch?v=QoEOFP6ukNY
Now I run the MMM 2200 combo on 6s using 2 5000 3s1p 25c zippy lipos and can say it gets down and temps are much better......
In my opinion save for the brushless and lipos first then upgrade what breaks....The 3905 has much better trannys and diffs then the old max and can take a beating......so far my drivetrain hasn't given me a single problem and the only parts on my truck that broke were due to my bad driving......"not saying you wont break anything" but I figure I would share my journy with you and maybe save you some time an money......
I wish I got to where I am now sooner