New build won't boot (1 short post beep)

Can you look in your motherboard guide/book that came with your motherboard and see what 1 short beep means?

Yes, RTM and see what one beep signifies. Also, just for giggles, try hooking the monitor to the GPU. Just because you (probably) don't have the drivers installed for the card doesn't mean that the mobo isn't still sending the video signal through it.

I stripped everything out, and started putting it back in one by one.

So far I've got everything in, except gpu (no output from either onboard, or gpu when it's in the pci slot, without it onboard works fine). I'm guessing that because the gpu is detected, it's defaulting to that, but because theirs no drivers it's not working? sould the onboard work at the same time, or is it an either or)

And my WD HD isn't showing up in the bios  

I moved away from using any gsata ports, not sure if that made any difference though.

I'm making progress though  

One beep for my board signifies a-ok.

I figured that's what one beep meant, as that's pretty standard. It's the POST beep (Power On, System Test.) Now, the GPU - pretty much every single time I've put a GFX card in, it's worked without the drivers - after all, if it didn't, how would you then see what you're doing in order to install them? Generally, it works on a low-res, default setting until you install the drivers, but it will still display. If it's in the slot, the mobo will default to it rather than the on-board. Does your card have an extra six or four-pin power connection? If so, did you plug it in?

The HDD not showing up is a biggie as well. Check your bios and make sure that you have everything enabled. Also, check other SATA ports. I've had a few mobos that, if the drive isn't plugged into the lowest-numbered port, it won't show up. Try another HDD if you have one.

Got the graphics card up and running, found a setting in the bios to initialise pci-e and then onboard. It was set the other way around.

Just the HDD to go now, I'm adamant the drive is fine (i'm really not). Anything i should look out for in the bios in regards to sata hdd's?

I've got a sata optical drive & ssd, and they're both working fine.

A couple of unlikely, but obvious things to check -

1.) Make sure the jumpers on the drive are on master rather than slave (not usually an issue these days, but you never know.)
2.) Is it by any chance on the same power wires as your DVD drive? (as in, you have a number of wires coming out of your PSU, and several of them will have 2 or more sata/molex connectors on them.) I have had it happen before with a weakish PSU and a powerful DVD burner and a high-speed HDD that there wasn't enough juice to run them both. Again, unlikely, but it's worth a check.

I've tried removing the power from the optical, so it's only the HDD on it, but no luck.

I tinkered with the bios a bit, but no real luck. The HDD has shown up once in the boot menu, and then in the bios in the next boot, but since then, no luck.

In the AHCI bios, it shows 6 ports, 3 devices. And then it hangs on whatever port my HDD is currently plugged in to.

I re-ran the windows installation, and it did detect the disc. However it showed up as one partition of unallocated space with 0mb free of 0mb.

I can hear the disc drive with the power on, it sounds like it's constantly seeking.

The drive has no jumpers on atm.

Sounds like a bad drive, unfortunately.