Try seeing if it will line up without the I/O Panel in place. The I/O Panel can often be a bit painful. If it does line up with the Panel removed then take the panel and push the little tags that are sticking up into a better position to accommodate the board.
Lay the case flat on its side. Line the board up with the Panel. It will resist. Look at the panel from the back of the case to check that the board is not been inhibited. It does take a reasonable amount of force. Push the board by placing the fingers of your right hand against the right hand edge of the Motherboard. Once the Motherboard is in place insert a couple of screws. Once the screws are in it should be easier for the rest.
A lot of the screws didn't line up perfectly but I just went with it. All 9 screws in place, I can plug everything fine into I/O panel and the board looks pretty straight with the tower standing on its side.
I pulled off the side panel to inspect what I could see on the back of the mobo. One of the mounting holes appears to have some scuffs around the hole (but not on any tracers) and everything else seems normal.
One thing I did notice while back there though, there appears to be a tiny yellow dot on one of the tracers near my CPU heatsink backplate. Never noticed it before, and pretty sure I did not scuff or grind anything there, there are no "scratches" nearby, I think a tiny bit of covering or whatever just came off. Should I cover this with nail polish eventually?
The only other thing I'm paranoid about is that all of that screwing and unscrewing loosened the brass standoffs, which I had screwed in quite snuggly. But...I'm sure I just worry too much.
I'll tell you one thing: they don't make it easy. Mounting the motherboard made me even more nervous than installing the CPU heat sink. Building computers is scary.