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Assuming the battery was disconnected, the ECU has to re-learn some parameters after having lost power. Give it a few cycles to sort out your throttle pedal and such.
You would have to try really hard to overfill the transmission. I'm sure it's fine.
Clutch mechanism is self-adjusting. It's possible to improperly adjust the pedal throw but the worst outcome is a slipping clutch. Did you adjust the pedal?
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