Q: Car shutting off

I have a check engine light for LOW EGR FLOW, which I assume is cause from a clogged intake manifold that I wanted to clean up but haven't been able to take off due to a stripped bolt. Also, my transmission is in limp mode and I have been driving like that for a while since I don't have the funds to take it to a transmission shop. So I've been just driving with a car with those two trouble codes. It did have an idling issue but once it was warmed up it wouldn't shut-off. Long story short, my car battery died the other day because I left the lights on and it got jump started backwards (they were placed backwards on my car). After doing it the right way, my car started and everything seems to be working except now the car will not stay on if I'm not keeping my foot on the gas. It's acceleration is really poor now, and even in Park, it will shut off from idling. I definitely know something electrical got shorted out, but I wanted to know where I should start looking for the problem.

My car has 160000 miles.
My car has an automatic transmission.