Think my ASRock might be failing

Ok guys. I'm having a bad problem.
I built this comp about 1.5 years ago and It's been giving me some scary problems.
build: PNY Nvidia 560ti asrock z68 Extreme3 Gen3 Motherboard Corsair 600w PSU 8gb patriot ddr3 ram intel i5 2500k sandy bridge
what's been going on:
Applications like firefox, itunes, windows explorer, Skyrim, steam, internet explorer will lock up. Games will simply freeze (audio will continue) while windows apps like the broswer or media player will kick back a "not responding error". Whenever it happens to one app, it happens to all of them. I can't bring up the task manager. Usually the computer will just BSOD and attempt to restart a few seconds after the crashes happen.
Sometimes the computer can reboot, but more often than not, I get a "BOOTMGR is missing. Press CTRL+ALT+DEL" error and have to power down the computer for a few seconds before I can restart it into windows.
What I've done to troubleshoot (starting with least likely culprit):
-checked gpu and cpu temps. Some were very high so I cleaned the heatsinks/fans with canned air and then reapplied thermal paste. Temps are very normal and stable now. No change in above situation
-Removed gpu to test onboard graphics. outcome: no change (aside from not being able to play graphically intensive games duh)
-ran memtest 86+. Outcome: zero errors after testing complete
-bought replacement HDD (needed one anyway). Outcome: put win7 on new hdd and downloaded a few programs (steam, skyrim, firefox) to test basic computing. Same issues, no change
SO I think it's either a component on the mobo has fried/gotten messed up (Sata controller? something else?)
Or my Power supply is going bunk.
This morning I switched the PSU cable powering my disc drive and the one powering my new hdd. Same issues.
Can someone help me?
it all happens at random, but it seems to happen more when the HDD get's taxed. (program installation, loading scenes in games, etc).

Have you looked for a bios update for this motherboard? "BOOTMGR is missing" means that Windows can't find to boot file on the hard drive. Is the CMOS battery on the motherboard good?