Okay, that's quite a list; a lot for us to mull over! Did all these come on at the same time, all there after the CEL first came on; or has the CEL been on for a while and codes have been slowly "accumulating"? Has the vehicle operation changed suddenly? Has there been any recent repair or maintenance work done just prior to the CEL coming on? Any other incidents we should be aware of, like recent collision damage?
Have you gone back to the Aamco shop, to see what they have to say about all those codes; especially since so many are related to the trans? None of the codes were new, coming in only after the timing belt? There are so many codes, some seemingly unrelated, that I wonder if all the electrical harness connectors were re-attached correctly during the trans change? (That's why I asked about "collision", as that is the kind of event that can produce seemingly unrelated damage/problems.)
oh this does look like a bad wiring after tranny change or timing belt. Evap code will never go away so start there. But this smells like Bill said, bad remount. Is car still under warrantty for this particular fix at ammco or is it to late, would like to know. If u got codes u have a scanner , can clear them, see what comes back, repost on these models, look for rust on filler tube for gas tank to get rid of evap code. the rest is a bad connection I a sure of this. Also look for cracks in gasket on gas cap, then check connection from primary harness to transmission. Hope we helped :thx