2005 TRANSMISSION FAILING.. MODLE # A5S 390R YZ

[Lost puppy]

2 Years ago I bought a 2005 X5 with 122,000 miles on it. Now It has 166,000 miles on it. For the past few months my service engine light has been on giving me fault codes about misfires and running to Rich or to lean bank 1 bank 2 etc and other engine related codes. yet the engine ran fine. The alternator completely died about 3 weeks ago and after I replace it I cleared the fault codes and everything was good. Two days after that I got a fault code of p0735 stating "Gear 5 incorrect ratio". The transmission started to slip and not go into 5th gear and it would go into fail safe mode. I shut off the engine for a few minutes and then start it again the fail safe mode light will be off and I can drive it like normal however it will not go into 5th and then it goes back inyo the failsafe mode and now I have lost reverse. My question is did the low amperage or voltage output from the alternator wipe out any of the electronics in the transmission. What would be the best way to go on fixing this problem?. Do I replace the transmission with one from the dealer at $5,000. Which would include the torque converter but not the 10 quarts of lifetime fluid at $500.00
Have my transmission rebuilt at $4,500.00
Get a rebuilt one from a parts house that I don't know a thing about it for under $2, 000.00 or so and hope it will work and for how long because I don't want to go through this again down the road. Has anyone experienced similar problems with their transmission please let me know because I'm thinking of replaceing or rebuilding it. Or am I thinking the wrong way and not seeing something. Any input on this would be greatly appreciated.