Windows 7 Boot Problem at Win7 Flag

I have 2 HD's with OS Win7 on both(dual boot). About 3 weeks ago my PSU (Cooler Master Real Power Pro1250-Watt Power Supply - SLI Ready, 80PLUC, 135mm Fan) started making a noise around the fan area. I noticed a lot of dust in the vent and blow it out and the noise went away a couple of days later. The next week, upon rebooting my PCto 1/2 dual OS (WD Blue 1 TB Desktop Hard Drive: 3.5 Inch, 7200 RPM, SATA 6Gb/s, 64 MB Cache) it stayed at the Windows Flag screen. The flag was waving(not frozen), but never completed the boot. I then pushed the reset button after waiting 30 min to boot to the 2nd HD (WD VelociRaptor 300GB HardDrive WD3000HLFS - 10K RPM, 16MB Cache, SATA 300MB/s) with windows 7 alsoinstalled and it did the exact same thing. I tried safe mode on both and itnever completed the boot. I did repair on both HD's and it will not boot to the1st HD (1 TB).

After many reboots it finally booted to the 2nd HD, but acted like it was lagging behind at times. I left the PC running in fear of not booting up and yesterday I found the screen blank, but PC running. I rebooted and now always sticking atthe Win7 waving flag.
Could the PSU be causing this type of performance or does it look like something else?

MyPC info:

Patriot EP 4096MB PC14400 DDR3 1800MHz (2x2048MB)
Intel Core 2 Extreme QX9650Processor BX80569QX9650A - 45nm, 3.0GHz, 12MB Cache, 1333MHz FSB, Yorkfield XE,Quad-Core, Retail, Socket 775, Processor with Fan

EVGA nForce 790i SLI FTW w/ Digital PWM Socket 775
XFX Radeon HD 6900

WD Blue 1 TB Desktop Hard Drive: 3.5 Inch, 7200 RPM, SATA 6 Gb/s,64 MB Cache
WD VelociRaptor 300GB Hard Drive WD3000HLFS - 10K RPM, 16MB Cache,SATA 300MB/s

First of all Starhowle mate why on earth have you got two hard drives installed both with it's own 7 OS?

That is for you to know and us to guess about I suppose but to me whatever drive it is trying to boot from sounds very sick (the Blue) and the velociraptor sounds not much better.

Now I would try unplugging the Blue drive and just use the velociraptor to try and boot with. Now if you can get into safe mode please run these

https://www.sevenforums.com/tutorials/1538-sfc-scannow-command-system-file-checker.html

https://www.sevenforums.com/tutorials/433-disk-check.html< if necessary include the /f and /r in the command line as per Option2

If we can get the machine running seeing it is quite an older machine I would like to see that PSU tested out but it needs to be booted to do that. In future mate don't wait that long for something to boot because after say five minutes max I would be having serious concerns about it booting.

I also would like you to have a look at this
Troubleshooting Windows 7 Failure to Boot

Hmm interesting way of doing it though the only way I can see that working is selecting the drive through the BIOS . Gokay has probably the best idea in that case and you shouldn't need to have more than one drive