V6 hypertech tuner

[SeanK122]

Hey so I need help diagnoseing the real problem with my car. so I bought the hypertech max energy powerprogrammer 2.0 #2000 to tune my 2011 v6 and i got the car about 3 months ago. the only thing I've done to t was a muffler delete. for the past month I've done extream extensive research about how this tuner works on my car and if it will work properly and everything checked out once it came in I drove my car to empty my tank to fill it with 93. Went home to tune the car to premium and a couple other tweaks and then warmed my car up and tested it out and noticed a huge difference i thought. After driving it for like an hour I started to notice that my voltage was getting low. Didn't think anything of it a little latter it starts dropping dramatically and battery saver mode kicks on and my car turns off ABS , traction control, headlights, all my gauges and somehow the clutch started slipping and shifting on its own in an automatic. I got home safely somehow uninstalled the tune and put the car on the batter charger. The car ran but only on the charger. While the car ran it constantly "coughed" (it would idle at 600rpm then every 5 seconds stuffer down to pole 500rpm), didn't know why it was doing that, kinda figured it was part of the dead battery, found out that the battery hadn't been changed in 6 years. So then went and bought an brand new batter installed it car started fine and kept its voltage at first but still kept coughing. I than again reinstalled the tune After driving around for 2 hours the car kept only coughing and the voltage dropped from a little bit above 12 to 11 high 10s so I still have no idea what's wrong with the car. Me and a couple buddy's think that's it just da crazy Coincidence that this happened at the same time I tuned the car but we don't understand the coughing part and we think it may need an new alternator but not sure. Any tip or help or advice would be greatly appriceated this is my first car and It only has 49k on it, it shouldn't die this early