2003 BMW 325 I need to fix my wifes car

First of all I appreciate your help. My wifes car is doing the following:

I was in afghanistan when this started so I don't knwo exactly the whole background, however. I know my wife flooded the engine by driving through a gigantic puddle and stalled the engine. My dad then had to pick her up and tow her car and dry it out, but he is no mechanic hes a body man.

in the morning when you first leave the house the car is extremely hesitant, it feels like someone driving standard for the first time, but this car is automatic. When you're driving, it sometimes does this even in the afternoon or after the car has been driven for long period of time.

when I cam back home, I changed the oil because she had not had it doen in a long time, but I couldnt get the oil filter out so I left it. I know bad. Anyways its been driven a 1500 miles like this.

one day the fail safe mode came on I took it to a transmission place and he gave me one set of codes, then I took it to the mechanic and he gave me a separate set of codes. Here are their combined findings.

143 tank-leak, 142 module fault
227 fuel trim bank#2
228 fuel trim bank#1
243isfire #6 cylinder
053 gear monitoring#3
p0313
p1393
p0174b bank 2
p0171b bank 1


im broke and I cant afford to fix this car at the dealership. What can I do?