Can't clear codes P0123 and P1605
 

My 2001 Accent (Manual Tranny) with 95,000 miles needed the head rebuilt due to the timing belt slipping and making a mess of the valves. The car threw no codes before the mishap and ran pefectly but now shows the codes P0123 and P1605 after the rebuild. The shop that did the work said they spent 5 hrs trying to figure why these codes are showing. They swapped out the TPS which didnt help. I'm not sure if they swapped out the acceleration sensor. Anyway, since I picked up the car,it was idling low at about 500 RPm and fluctuating in neutral (remember its a manual). In the week that followed, the car wouldn't start a few times which I found out to be a loose negative terminal on the battery. Since I fixed that problem, the car idles at about 1,000 RPM when I start it but then jumps up to about 2,000 once it's warmed up or if I downshift and then throw it in neutral! And yes, the same 2 codes show up on my scanner. HELP!