My guess would be the old favorites:
EGR valve / solenoid
When the engine is missing slightly, it will also feel erratic in the tranny, making you think it's a tranny problem when it isn't. An area I've had problems with on the LT1 is the spout where the coil wire connects to the distributor, behind the water pump. On two of my LT1s, the spout had cracked or broken, causing it to arc in there, and I couldn't see the arching even in the dark because of the location of it. If it is cracked, the cap has to be replaced, meaning pulling the Opti. If that's the case, just do the entire distributor and water pump at the same time, since it has to come off, too. From Dal, the Opti is just under $200, and the waterpump is another $100. I think I paid $330 shipped total. If the wires are old, do them, too if you can. Also, since the AIR pump is in the way of the wires, delete it, too. Sounds like a lot of work, but it's not that bad.