I would reset the BIOS to defaults. If you didn't plug all the drives back into the exact same connectors on the motherboard, you might be confusing the BIOS and/or Windows.
You're supposed to use the I/O backplate that comes with the motherboard and not the one that comes with the case. That's the 11.5" by 5-6" metal piece where everything hooks to the back of the comp.
There's no way to tell for sure, but you may have broken the thermal paste seal of the CPU heatsink and the CPU.
The fan on the CPU cooler must be plugged into the white (in your case) CPUFAN header on the motherboard.
Semi modular power supplies have some cables permanently attached to the power supply and some that are removable. In non-modular power supplies they are all permanently attached.
You must have all the motherboard screws in place, no more, no less.
I would reset the BIOS first. Circled in RED are the pins to Clear the BIOS (reset it). Short the two pins together with the power off, with the power supply plugged in but the switch on the back of the PSU turned OFF.
Short the pins together with a screw driver for about 30 seconds. Then remove the screw driver, turn the power supply switch (on the back of the PSU) back on, then boot the computer.Are those unknown cables, hooked to the power supply or the case? They probably aren't important right now.
/e The only thing I can think that those two unknown cables may be for is for a floppy drive?? As far as I can see you have everything hooked up properly.
Let me know when you have reset (cleared) the BIOS and if that improved the boot time.
This post was edited by Ghot on Feb 8 2018 10:50pm