2001 Hyundai Elantra Multiple Misfires and Transmission Issues???

I have a 2001 Hyundai Elantra, I've had it about 2 years already. It only has 64k miles on it, and I just dropped $350 in repairs and an inspection last week. So yesterday, driving over 40 miles to get to my doctor, my car started bucking like crazy and shaking when I hit the gas, and then the check engine light started flashing. I eventually broke down on the side of the highway because I couldn't make it up a hill it was bucking so bad. My uncle is a mechanic and came and towed me home and is going to take a look at my car, but he doesn't have a lot of free time so it might be over a  week.

I just want a little bit of info so I know what to prepare for repair-wise. He checked the engine with a sensor and there were 8 codes. Cylinders 1 & 2 are misfiring, and some error for the transmission came up. The others just said misc. errors. My uncle won't charge me for labor, so what am I looking at cost wise for parts? And what could it be that's making it misfire? VAnd what sort of things could be wrong with the transmission? Any wild guesses would even be appreciated, I'm completely in the dark.