What "battery powered" microphone are you using? Is it a pair of mics and a battery box? You said you're running into the TRS inputs... are you using Sound Pro's 1/8" > 1/4" TRS adapter or something different?
I think 3 hours is a decent running time for the Microtrack without an external power source. Recording to wav probably gets your more battery life than recording to mp3 because it takes less processing power. You might get more battery life running at a lower sample rate, though (p.s. what does 44.1/96 mean? Do you mean 24/96 or 16/96?)