any techs on here please help, many problems, transfail safe again

[IMOLAredNC4.8is]

My 2004 X5 4.8is has been in the shop now for almost 4 weeks. The car is [COLOR=blue ! important][COLOR=blue ! important]reading[/COLOR][/COLOR] DSC 4x4 Inactive, Self Level Suspension Inactive, Tire pressure light, ABS light, lose of [COLOR=blue ! important][COLOR=blue ! important]power [COLOR=blue ! important]steering[/COLOR][/COLOR][/COLOR] and the radio will cut in and out and the nav screen will flicker on and off like crazy. If I am driving down the freeway I have no problems at all. As soon as I get off into stop and go traffic thats when the car starts going crazy. All those warnings and faults will start popping up almost everytime the car is just sitting at an intersection or stop. I will pull away and the car will barley drive. Sometimes i get transfail safe prog message too. I took the X to hendrick BMW they could not get the car to reproduce any error messages so they replaced the EHC module thinking it would maybe solve the issue. 1000$ later the car is doing it all over again. I thought back to right when the car started doing this. It all happend after i had my [COLOR=blue ! important][COLOR=blue ! important]amplifier[/COLOR][/COLOR] turned all the way up on my after market system. We went and had the alternator and batter tested today, both came out fine. But we were told the [COLOR=blue ! important][COLOR=blue ! important]battery[/COLOR][/COLOR] had a very low charge to it. We disconnected the amp and subs about 4 weeks ago. I was told that the battery had been drained down to a very low charge from the after market amp and the alternator would not charge it back up to its full charge it would just maintain the low voltage reading. So my question is if we charge the battery back up completely will it run fine if the car is working off of a fully charge battery? The little eye in the battery was completely black. Other question is that if the battery voltage dropped to that low point will it go right back to that low point again and not hold a full charge? And is it possible that if the car is running on such low battery power it will cause all these faults to come up? Please help and thanks for your time. (oh and the only time these faults come up is when the car is driven around town in stop and go traffic) also i was doing some research and ill add that i did replace my brake pads myself and now i still have the red brake light on my dash. Someone said the sensors might need to be replaced