Can't clear brake codes

I have a 2005 with 180k miles - ran great - no problems - started it up the other day and got 1/2 mile from my house and got the red triangle, check engine, skidding light, brake light, VSC and ABS light. Turned around - took it home, shut it off and couldn't start it again. It would turn on, but wouldn't really start up and I couldnt shut it off normal way. Had it towed to my garage (non toyota) They got lots and lots of codes ( C2318, C1259, C1310, P3000, P3030. ) and said it had the original batteries - so replaced 12V, didnt do anything , so replaced Hybrid battery. Car seems to runs great but still have the brake, ABS and VSC light on, they could not be cleared. The computer said that it was not communicating with the system. Have codes C1203, C1345. They thought maybe it would all clear after we drove it 100 miles. No luck. The fact that these lights came on with all the other lights originally leads me to believe (and hope) that it was something that got screwed up when the hybrid battery died and not actually a brake problem. Any ideas?