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VW New Beetle Convertible Issue

Hello. My wife’s VW 2004 Beetle Convertible was hit and run last winter while parked in front of our house. Most of the driver’s side had to be replaced, though the windows and convertible roof did not. The body shop kept it for 4 weeks, replacing the driver door with a used one. Now the window doesn’t slide up to it’s proper position everytime. Also, with the warmer weather we’ve started letting the top down on occasion. The little metal wings at the back on each side of the passenger seat come up into place when the top disengages and lifts to the back of the car. However, once the top is in place on the trunk, the little wings do not slide back into the car body like they are suppose to. This results in a constant warning sound and lights when driving the car. Also, my wife thinks the top doesn’t lay flat on the trunk when open.

I intend to take it back to the body shop, but they hemmed and hawed about the driver side window, so I’m sure they will say it’s nothing they did. My question, what might they have done to create this problem? Messed up the wiring in the replacement door? Messed up the computer system when they disconnected things? Any ammunition anyone can offer, or advice for fixing will be greatly appreciated. Thank you.