what i've been told is that after the ecu is reset (new battery) it is best to start the car and let it idle for 10-15 minutes to learn/ set up what it needs to.
I to had the crazy low idle, and stall once or twice when i depressed the clutch while driving. happened after i had the battery disconnected for a period of time. just keep driving it and it should correct itself. those issues only ever happened during the first 100 miles?