Msi motherboard usb connectors wont line up with holes

[twodogs_46]

Hello,
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?

 

[marcellis22]

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.