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Sounds like you've already done some solid work on the sunroof, nice job sorting out the inner lining too.
Now, about the non-starting issue after the battery went flat, you're definitely on the right track by planning to replace the battery first. A weak or deeply discharged battery can cause all kinds of strange behavior, even if it *seems* to crank the engine fine. Low voltage can mess with the ECU, fuel pump, ignition, and sensors.
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