Rezonance

I just recently did some work on my jeep after a rock took out my exhaust pipe and my tranny cooler lines. On starting the engine the engine runs fine, but loud, on idle. When I test drove it whenever I let the gas off and I brake the rpms drop to 0 and it starts struggling and sometimes sets the check oil light before the rpms go back up. It was sitting for a long time before I started it up again... about 7 months maybe? I had to drain the oil to remove the exhaust (oil filter was in the way) so maybe there isn't enough oil on the lifters? The oil pressure was a little screwy before so I was thinking about replacing the oil switch anyway. Also, tranny fluid looks a little bubbly. Any comments that could help?