Thanks for the thoughtful responses.
The cheap MAF I took out and put the original back in after resetting and finding that it didn't help at all. Should I still get a replacement?
O2 sensors are probably OEM. I put 30-40k miles on before I had problems.
The transmission is/was AWD and the car does shift into 4th, I think with no problem.
I'll check the vac lines with carb cleaner, good idea!
I guess next step is getting the exhaust hole fixed... I just don't want to go to Lexus or a foreign car expert and get taken. Prior to the transmission replacement, my rear exhaust was hanging off and I had no problems like this. Afterwards, I had it fixed, but it didn't change anything. Still, perhaps the hole near the front was created while pulling out the transmission and is giving me problems.