Does anything that controls the idle and performance have a memory? After disconnecting and reconnecting the battery, the car runs horribly for the first 10 minutes of driving. Sputters, no power, idle can surge, etc. The longer you drive it the better it gets until the battery is disconnected for any reason.

Whole Story - my son calls me in the wee hours of the morning. He has the 240 '89 wagon at a friends house and is trying to start it to come home. However, it doesn't have any juice. I go over and figure out that it is only a loose battery connection. That explains why the radio had been losing all presets every once in a while. However, there had been no problems with the engine. It had run well.
Now, after tightening the battery connection, the car has juice, and starts but is running poorly (as mentioned above). My son also points out that it is REALLY low on gas. I drive it home and by the time I make the 15 minute drive home, it is running much better.
I decide that it might have sucked in some dirt from the bottom of the gas tank. The car is new to us and I am not sure how often the previous owners have run it low on gas. So, it is showing signs of a bad fuel filter and I decide to change it.
I change the filter and nick a whole in the gas line in the process. Have to cut and reattach the heat shrink fuel line.(that's a whole other posting) After getting all back together, that still didn't do it.
I then look up some symptoms and decide that it might be a dirty throttle body. I bought the right stuff and cleaned that. That didn't do it either. However, in the process of all that, I noticed how it always runs bad after working on it but gets better the more you drive it.
Sorry about the long story but I want to get all the info out there in case it helps.
I am not a super experienced mechanic so please make any suggestions in terms a dummy can understand.
Thanks for your help.