Transmission, engine, can't tell what's going on....

'04 automatic, timing belt broke, have done all repairs. Ran fine for 3K miles since, but less bottom end power. So now it feels like the tranny is jerking/slipping. But, the engine is skipping when idling, and the tranny thing happens on hills with acceleration. Engine light does not come on when idling rough occurs (it's random). Engine light has come on twice when shifting occurred. ??? 158K miles, original tranny.

What was the code(s) from those CELs? Unless the code leads the way to fixing it, compression / leak-down testing might be a good next step.