I think that the only thing a dead battery would do is wipe out stored error codes. May or may not wipe out trim settings - I can't remember whether those are in flash or SRAM. Did you charge the battery with it still connected in the car. If you have a good charger that should not present a problem; but, if you had one of those rapid charge things I don't know how high the charge voltage gets, could present a problem; but, unlikely.
I don't have my service manual handy so I can't check to see if fuel trim is reset on a power loss. If it is and your car was running close to the limits on fuel trim before the battery was killed, the loss of trim may result in the engine running lean and suffering from some lean surge. 'If' it is trim, driving the car will gradually restore the trim settings and make the problem go away. If it does fix it self, I would be inclined to investigate why the car was running with so much trim.Personally, I think this is a lower probability possibility. If you have an early non DBW car, I would definitely be giving TomCat's suggestion a check and have a look at the EACV to make sure that it is operating correctly.
As an observation, I disconnect my battery every fall and reconnect it every spring and the car starts and runs perfect. Loss of power to the ECU does not normally result in operating problems. Something else is in play.