I've been desperately trying to fix this extremely annoying issue.
Once my computer finishes booting and lands on the desktop, it takes another minute or two to load all programs and the internet sometimes won't even work until then. The first program to load is GeForce Experience, if that helps.
Everything used to load up properly and nearly immediately.

Also, I've reset my computer twice today and installed the MSI motherboard drivers and on the first OS installation none of the wireless, ethernet or bluetooth drivers worked, even when downloading their newest driver on my phone, moving it to my computer and installing it. On the second OS installation, only the ethernet driver worked. I've reseated everything but the CPU in my computer, even the wireless Killer AC 1525 that comes with my MSI X99s Gaming 9 ACK.

What I've tried:
Moving USB devices to other ports
Unplugging ALL USB devices (yes, mouse and keyboard included) and even the ethernet cable out of desperation
Wiping all drives and re-installing Windows 8.1 64-bit and installing all Windows updates before doing anything else besides installing motherboard drivers
Re-installing OS 3 times
Re-seating all drives and GPU.

This is really upsetting me. I've put loads of effort into this 2-month old custom build and I'm not able to enjoy it.
I need it to work as fast as possible as I need it for school reasons.

Thank you VERY much for any help.