No spark after charger start feature was used

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My girlfriends X5 sat for a couple of days while I was away for work. When I arrived home I replaced the capacitor in her key fob since this had been giving her problems. It was not working as either were the interior lights. After reading more and talking with her about some of the problems this car had been having I believe it was most likley in transport mode after being jump started months prior. She finally told me that is when all the stuff stopped working.
After replacing the capacitor I attempted to re-initialize the key ( before I learned about transport mode) without any luck. The battery was weak again so I put my charger on it that has a 50 amp jump feature. It started up right away, but as soon as i disconnected the charger the X5 motor sputtered to a stop. I tried to start it again but the motor just spins freely. It has fuel since I can smell it every time I try to start it. I have checked all of the fuses in the glove box and in the pass side rear- all were fine. I tried to scan it for codes and there are none stored. I have disconnected the battery and let it sit over night while the battery was being trickle charged. The battery was load tested and appears to be descent. it has about 600 cca.

Have I fried the computer??? Any sugestions would be appreciated.

Any Ideas guys? Is it possible i smoked the computer? Any other things I could trouble shoot? Am I misssing something or do I need to haul this junk to the dealership?

A little more info.
2004 X5 3.0w 76,000miles