El Capitan won't boot without USB after CPU cooler installation

[hamiltrp]

The usual 'please forgive my ignorance' affidavit applies here, as I'm new to this. After doing all the prep work (bios settings etc, disconnecting all PCI/USB devices) I successfully installed El Capitan using UniBeast, and then applied MultiBeast after, and had it booting successfully from my internal HDD (only one drive, single GUID partition, OS Ext Journ - NO WINDOWS ANYWHERE). Had it booting a number of times stably, then I installed a new CPU Cooler (Cooler Master Hyper 212 EVO) so I could overclock (haven't changed FSB or any values in BIOS yet), and now it won't boot from the internal HDD anymore. It hangs on 'scan entries' for a good 2 mins and then finally goes into the Clover Boot Manager screen with the lime green clover and light grey background. Can still manage to boot into El Capitan using USB and then selecting 'HFS internal', but would prefer not to continue this way, obviously. Tried mounting EFI and edited config to ensure default volume was the same name as my internal HDD. Any help would be greatly appreciated!

Specs:

Gigabyte MoBo GA-EP45T-UDP3 with AWARD BIOS
Core 2 Quad Q9550 (Cooler Master Hyper 212 EVO)
8 GB Crucial 1333 RAM
Seagate Barracuda 7200 RPM 500 GB connected via SATA
ASUS NVIDIA GeForce 9800 GT 512 MB RAM (have set MultiBeast to properly work around this, I believe)

THANK YOU!

 

[KONKY1]

Check your connections are connected properly, look at all internal devices from power supply to hard drives.