Diagnostic help needed! '08 TE250

My bike up and died on me in a similar manner it did last time, and it ended up being a bad battery. I was riding, and it started to bog. Low fuel light was blinking on/off (and I clearly had 3/4 or better), and then it died. I had no instrumentation display with the key on, and needless to say, it wouldn't turn over or do anything. Same thing happened before, and I had been riding some pretty knarly trails. Best i can figure on that is that I didnt pad it sufficiently on top, as I was warned to do. So, I loaded it up and brought it home.
Battery was only show about 9 volts when I first took off the seat today. Connections were all good and tight, and there was no visible damage or blown fuses. I put a battery charger on it, turned the key on, and the instrumentation came on and the fuel pump primed. I turned it off and let it set on the charger for a few hours; but, when I checked it again, the battery still read 9 volts. Took the charger cables off, and no instrumentation or fuel pump priming. Then, I hooked some leads to my Jeep's battery. Everything came on when I turned the key as it should. I hit the starter button, and it fired up instantly as it usually would. I pulled the leads off, and it died within a couple of seconds, and went back black on instruments.
So, having just bought the battery on August 24th, I took it back and they exchanged it. Brought it home and put it on the bike. Everything came on when I turned the key, BUT now the dang thing won't start! It turns over good and strong, and I checked the spark and it's fine. No fuses are blown (at least the 5 I know of), but it seems like it isn't getting fuel. I have a shop manual PDF, but all it really talks about on diagnosing the fuel injection is hooking it up to iBeat, which of course I don't have.
I'm at a loss of why it would have cranked up and was running fine (at least until I disconnected it) when I had it on jumper cables, and then turn around and not run when I put the new battery on!
Does anyone have any ideas, tips, or suggestions on what I should do next? Out of all the times I tried it, it made one single "burp" of firing off.

It has a Power Surge 6x on it if that helps the diagnosis. It seems to be powering up fine

last time this happened, I asked you for the voltage while idling. with the new battery, you said: 14.56v (and I'm assuming this was NOT when the battery was hooked to the charger at the time... right??).

still, this sounds like a bad charging system. assuming you're putting out the 14v at least some of the time (please check), lets take a look at your connections (loose? clean?) and take a hard (hard) look for small rubs or slight burns in the wiring.

start at the battery, starter relay, regulator then stator. then look for tight spaces, turns and edges where any wire might get cut or rub.

good luck.

Like trenchcoat85 said, check your wiring thoroughly. Our injection needs at least 9.5v to operate. Lay the bike on its side and check the stator pickup and wiring. Make sure there is no build up on the magnet.

If you have ibeat I would go in and take a look at everything