im pretty sure i have your answer. this is exactly what happened to me last sunday coming home from the new york motorcycle show. i was gonna make a post but with everything going on i had no time. i have a 03 4.6 that just hit 102k. about 15 miles before the transsafe i got the battery light. once all lights light up the foot pedal was dead and once i turned it off, trying to restart it sent all electronics into freak mode. luckily i was only 5 miles from home. So i had it taken to the dealer for a diagnostics. what they came up with was no egs faults stored but various low voltage faults. trans program may have been set by low voltage. first thought was alternator. they offered a bosch rebuilt one with a 2 year for 1200!! sounded a little crazy to me so i had one overnighted to the dealer for them to install. i found someone in florida with a bosch rebuilt one with a 1 year for 400 plus a 160 core charge. dealership charged 383 to install and 121 for the diagnostics. it runs perfect now. i was bummin big time though when i saw the transsafe come up. so overall it was around a grand to fix. oh well. good luck with your situation. really sounds like an alternator to me though.