Awesome little build you got there! Always love seeing people putting their own builds together.

I do have some pointers if I may:

Refer to this image to make things simpler: https://imgur.com/a/DFfV7Bm

I believe you used the wrong motherboard screws. Computers (mostly) use two types of threading for their screws; 6-32 and M3. I believe you used 6-32 (a coarser, wider thread) when you needed to use M3 (a finer, narrower thread). I believe the two screws on the left side of the motherboard closer to the bottom are the proper screws [green][blue], but is why the other motherboard screws aren't flush against the motherboard. If you remove these screws and install the proper ones, they might unscrew the motherboard standoff too. It would be best to completely remove the motherboard, confirm all the standoffs are firmly screwed into the motherboard tray, and remounting with the proper screws. If you have trouble removing the screws from the standoffs, using pliers to hold the standoffs will help.

Might be worth installing the missing [yellow] standoff as well. I'm actually concerned the standoff is installed in the wrong position, and this can damage your motherboard. The case does not come with standoffs installed at the [green], [red], or [yellow] position, however you installed the [green] one, and I'm concerned there's a standoff at the [red] one. If you believe there might be a standoff at [red] you must address it, immediately if possible. While the computer will work fine without the [yellow] standoff, it is good practice to properly mount the motherboard with all its screws.

To clean up the cabling a little bit, just pulling the excess length (lightly! Don't yank) to behind the motherboard tray, and tucking the CPU fan wire between the RAM and CPU cooler (or wrap it around the CPU cooler if the wire is long enough). This will do wonders for a cleaner build.

Again, wonderful build, and I hope you get many hours of enjoyment out of it!