I case you aren't aware, the battery box isn't a preamp. Somewhere you need to bring the mic level signal up to line level. Personally, I would never let a consumer piece of gear do this process for me. I have owned portable MD recorders and an M1 and I wouldn't use the mic-in jack on any of them. Hence, I would never even consider the possibility of maybe thinking about pondering the fact that the JB3 HAS a mic-input and ESPECIALLY never consider the use of it. More simply, get an outboard pre. Or use the JB3, whatever you want.
As for the mics, the response on the cards sucks donkey balls. If it's between those 2, go omnis. ALso, check out the Dynamic Audio "Binaurals" if you are looking to go that route. If you are willing to spend $200 on mics and power, I can give you much better advice in the stealthing realm.
good luck!
peace
~schwills