Ok so I'm here looking for possibly a little help. For about a week and a half now I have been having issues with my car going into 2nd and 3rd gear. It also has went into limp mode 3 times within the week and a half. It all started when I put my stock airbox back on. When I did this I disconnected the battery and I cleaned the MAF sensor. I put the battery back on after about an hour and a half and started having problems the very next day with rough shifting into 2nd and 3rd. The 2nd the car does a slight jump into gear and then into 3rd is a rumble under my feet. It would not do it all the time but my first thought of course was the trans is going. I also noticed that when this happened it felt like the pressure was lower and the car felt like it was lacking power. I put my intake back on which is the Roush intake. 07 GT btw. No mods except the intake which is supposed to be no tune required. I do have borla atak axle back also. So on with what's going on. With some research I learned that my issue could be electrical so I had the battery tested and it was bad and under warranty so I replaced it. Alternator is good, according to autozone atleast but who knows with them. After the new battery it seems better but it still will shift rough into 3rd at times but not nearly as bad and not nearly as often so the battery did help which is why I keep thinking I have an electrical issue. I have 99000 miles on her and I have had the car 2 years. I have had some electrical issues already. This is battery 3 and I replaced the alternator about 2 months after getting the car, I was in a desperate moment so I bought a duralast alternator.

Other than that it's great other than also new brakes but that's normal stuff of course. Everything works very well and it always has ran super smooth, trans has been seemless up until the recent events. I have noticed also that when I started before to get the horrible shift into 3rd it would come with somewhat labored steering and what sounded like slight brake squeaking at the front wheels which would change with pressure on the brakes. All 3 of these things would happen basically at the same time. Could it be my belt? Could it be the alternator weak? Did I possibly just cause a major trans problem because of a bad battery? I'm likely going to take it somewhere very soon but I was hoping I could get some advice here. I do have a bama tuner which I haven't actually tuned the car still but I used it to check for codes today and it says there are no codes found, I tried it 2 days ago and I got the p1000.. Not enough drivetime basically. So the computer must be logging and saving the drive cycles or I'm sure I'd get the same code again? I have just put so much thought and time into this. I honestly think it's the alternator. Last time I had a battery go bad autozone said it was good... I said you're wrong, brought it home and took it out of the car and brought it inside. Charged it to be sure it was at full charge and walked away... Sure enough, it was dead 10 hours later. Thank you for reading and any advice will help

 

Something's definitely killing your batteries 'cause now you need battery no.4. You might want to perform an AC ripple test (there are videos in YouTube) to confirm whether you have a bad alternator diode, as any AC ripple current leaking into the electrical system can cause all sorts of gremlins. ​​​​​​

 

Are you the original owner? The reason I ask is that you said the intake was supposed to be 'no tune required' and many of those ended up needing a tune. So if you bought the car used it may have a tune on it.

 

Thank you for such fast responses.

I will try that test the next couple days and see how it goes. Couldn't happen at a worse time being the holidays
I think it is my alternator going crazy after driving a bit. I have a new belt laying around so I'm going to change it also though I don't think it's that.

The intake I put on and it's been great and never caused a problem. It is the Roush intake for 05-09 Mustang GT. It doesn't require a tune. I'm the 2nd owner and it has good service history. I doubt it had a tune because it was completely stock and being in California I'm not sure how it would pass smog and be registered for me to buy it

 

So I just wanted to update this post for anyone who may experience what I did. I am in disbelief right now. So for the past 2 do us she's been great. It's been progressive. So I'm not sure if the bad battery affected the trans mechanically but It appears that the new battery has fixed my issue. It is unbelievable if you were to be in the car and feel the difference. I did find something very interesting in my owners manual. Page 221 in the battery section mentions steps on installing a new battery which honestly I always just took 1 out and put 1 in. This time I literally had it disconnected for 5 minutes max which I should have left it off for enough time to clear the computer. If anyone else has this happen to them check your battery and look at page 221 in your owners manual, it's pretty surprising

This is the part mentioning the battery and trans connection
My next step is I'm going to just go ahead n take her to the electric dr 😂 I know a good one and figure out why my pony likes to eat batteries