Your question is not very clear. But if I read it correctly, You are stating you have already assembled your front sheetmetal and are assuming you have frame damage because things are not lining up? And now you want to send it to a frame shop to have it checked / repaired, and do not know weather you should leave your new panels on or not?
The answer would be take it to the shop as is with panels in place. It will give the shop a reference point
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