Have you checked the battery voltage and tested the alternator? If the old battery took a crap and the only thing you've recently changed I'd be more suspicious of the charging system initially. Check the voltage at the three + supply terminals on the ECU while cranking. If the voltage is dropping below 11v you've got power supply issues... whether or not the ECU is bad, it's power requirements are not being met while cranking.
As for the window, have you taken a meter and followed the supply to see where the loss is?
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