Msi motherboard usb connectors wont line up with holes

I installed an MSI Intel MB into a case that used to have an Asus AMD MB. Some of the mounting holes don't line up but my big issue is all the little connectors on the back are a little off position and some of them are inaccessible. Is it the case, or the bracket, or the stand-off bolts on the case?
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  1. You should have gotten a back plane plate to fit the new(er) motherboard. It does help with the grounding, but you can remove the ill fitting plate and run without it.
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