I'm pretty sure that the iRiver devices have internal (not exactly field-replaceable) batteries. The JB3 does seem to have field-replaceable batteries, with the possibility of loading more than one battery at a time (for 12+ hours of recording time).
The reason for using the digital input (over the analog) on your recorder is that your UA5 has already converted the analog signal to digital, so why convert it back to analog and then to digital if you don't have to?
A Microdrive is what the name implies: a tiny (1" platter) hard disk drive. I can't think of a single advantage of using a Microdrive instead of Compact Flash. The CF card will use less power, is less likely to cause electrical interference within the recorder, has absolutely no moving parts (so there's nothing mechanical inside to break if you drop it on the ground), and because there are no moving parts, the CF card should "never" wear out.
Yes, I'm a little biased, having owned more devices with moving parts (that eventually self-destructed) than I probably should have. Hard drives kinda suck for analog recording but I don't see how they'd mess up a digital signal from the UA5. Still, you'll get better battery life from Flash memory. Moving parts are for bicycles! GO SOLID STATE!