As others have already said, battery, and this is the clue. The cause is letting the battery sit uncharged for a couple of months. Lead acid batteries don't like that.

As far as disconnecting the battery while running, yeah, that is a no-no. As said, it causes a voltage spike sometimes called "load dump". In theory, the electronics of the car are supposed to be designed to tolerate it. In practice they may or may not. Hopefully you dodged the bullet on that. Good luck.

__________________
1998 C230 330,000 miles (currently dead of second failed EIS, yours will fail too, turning you into the dealer's personal human cash machine)
1988 F150 144,000 miles (leaks all the colors of the rainbow)
Previous stars: 1981 Brava 210,000 miles, 1978 128 150,000 miles, 1977 B200 Van 175,000 miles, 1972 Vega (great, if rusty, car), 1972 Celica, 1986.5 Supra