I had the same issue (from a month ago), eventually contacted support, and after many troubleshooting steps they decided to replace the mainboard (hasn’t arrived yet).
I have a Framework 13, Intel® Core™ i5-1340P, Windows and have the same slow startup + USB not working (even in BIOS) + No Bluetooth. However unlike @Agnes, my issue happens even on battery, and has fixed/broken itself twice.
@Nicholas_Shepard I tried disabling IO ports in bios, and the system now boots normally and bluetooth appears in device manager, however (as previously) it is unable to shut itself down. This option is under Security → I/O Interface (scroll all the way down) → External I/O Ports. Naturally this doesn’t fix the problem, but at least we know it’s related to the I/O Ports (support never told me to try doing this).
I think we should all post in this same thread to share information with each other, since we have similar symptoms.