Motherboard Error Or CPU?

I'm going to break down your post here as it seems to be a few questions in one.
Let's start with the RAM. From what I understand you have 4x4GB of RAM. The kit you listed, F3-14900CL9D-8GBSR, is listed in the QVL for the motherboard which is a good sign. The motherboard appears to support up to 32GB of RAM using the 4 slots it has (4x8GB) so this shouldn't be a problem. What we're left with is improper installation, a possible dead stick or two, and an unstated OS.

We'll start with the OS here. If the OS you installed to the SSD is 64-bit then you should get all 16GB of RAM. If you installed a 32-bit OS then you would be limited to 3-4GB depending on certain options enabled in the OS (Typically 3.5GB). This can also be effected by other things such as onboard graphics being provisioned a portion of the memory for it's own use.

Next up is improper installation. This one's simple. Just make sure they're installed correctly. When in doubt just take them out and re-seat them. Make sure the notch in the RAM slot lines up with the notch in the RAM sticks. If they fit well the tabs on the RAM slot should snap in to place. The motherboard's manual has a basic outline of how to do this. The online version of the manual shows this as page "2-6" or Chapter 2, Page 6 which is page 64 on the PDF.

Last up is having dead hardware. I left this one for last as it is quite a bit more labor intensive and time consuming. If you followed the above and are running a 64-bit OS, the RAM's been properly seated, and are still showing less than 16GB total RAM (12, 8, or even 4GB) then we need to do some digging. First, I'd suggest using Windows' built-in memory diagnostic. It takes a while to check your memory but it's very simple to run and will report if there's an issue. If that passes then it's down to testing individual sticks. From what I understand looking at the motherboard's manual (1-7 or page 23) the system will only work using a single stick if it's installed in slot DIMM_A2 (2nd slot away from CPU). You'll be booting from each stick and checking in BIOS to see if it's detected properly. If you have a dead stick you will know right away with this method as the system will refuse to boot with a bad stick. If you get through all 4 individual sticks then you're on to testing them in pairs. If you go through all variations of the pairs then the final test is all 4 sticks at once. If you put all 4 sticks in and finally have a problem then try shifting the sticks around. This is where it gets time consuming, though. See, you're actually hoping that this test will show you which stick is bad but sometimes you'll have one that doesn't play nicely with the others. Although, this USUALLY shows up with the memory diagnostic. If you make it this far and still have trouble then you're looking at more comprehensive tools to test the RAM. Memtest86+ is my go-to for this. If ANY errors show with Memtest86+ then you indeed have a problem. Typically it will tell you which stick it is as well. Either that or it says what size where the error shows (example: 5,324mbyte or 5.2GB which should be DIMM_B2).

Now for the rest of the post. Can an SSD cause the RAM capacity to shrink? No. Although, when you formatted it did you install a 32-bit OS to the SSD? If that is the case then certainly the 32-bit OS is the reason for your 'missing' RAM.

High disk usage and long response time on an SSD. This can be a multitude of things and I've already written a book just to test the RAM.
Did you do a secure erase if possible?
Was the format NTFS (assuming Windows) or was the format performed by Windows OS installer?
Is the BIOS set to AHCI mode for the SATA bus?
Does the OS see that it's an SSD? This sort of coincides with AHCI mode.
Does the OS have TRIM enabled?
Lastly, the high disk usage could be a result of a lot of swap file usage compounded by the RAM issue. Unfortunately, if the RAM capacity is low then the OS will use your storage drives as virtual memory and this will result in high disk usage and writes.

Ah, that's unfortunate. That was going to be the last thing to check after making certain the RAM was fine.You'll probably be looking at getting the motherboard repaired by Asus if that's the case. The CPU detection issue is most likely something with the socket. I've actually had a motherboard with a bad socket before but this one was much more terminal (no POST, status lights next to CPU and RAM). Cost about $100 to have Asus fix it outside of warranty.

Interesting... The picture of the pins is too muddy to really make out any details (besides, they're quite small anyway). The pad on the CPU though. Hmm, I wonder if that's residue of some sort on the pad. Have you tried lightly scraping it with your fingernail? It suggests that the pin associated with that pad might also be bent slightly. If you can determine what pin that is it would just need to be bent straight a tiny bit.

I'd only suggest doing this if you really think these components are going to head for the trash. I'd suggest trying a CPU from another computer first before messing with the motherboard pins.

It's difficult to discern from the picture. It could be corrosion (usually just discolors though), etching (partial pin contact + electricity arc), leftover residue from manufacturing (kind of rare), or something that ended up on the pad somehow. I've seen a rather large dust bunny pinched between the CPU and the socket before. It's probably not that but it's just an example. Hmm, perhaps thermal paste? I'm just throwing ideas out here.

According to the manual the 00 code on the Q-Code LED is not used.

PSU causing your motherboard to forget about sticks of RAM? I highly doubt it. The 00 code makes me wonder though. Not related to PSU still but perhaps have you tried resetting the BIOS to default?

Usually Asus but Gigabyte and EVGA are great too. EVGA's got great customer service.

EDIT: Q-code 63 looks to be related to RAM even though the manual mentions it's CPU-related. "CPU DXE initialization" http://www.tomshardware.com/forum/336587-31-motherboard-stuck-error-code-stands-initialized

Do you have any willing friends that could put your RAM in their computer to test it? It would be a simple way to rule out the RAM as the problem but I honestly think we've determined that it's CPU or motherboard.

It's unfortunate, this would be such an easy thing to figure out if you had known-good parts you could swap around. I've got a bunch of stuff in my shop but your particular platform is the rare exception. Swapping parts was how I learned something was wrong with the Asus Sabertooth X58 I picked up from ebay a while back. Took known-working parts and put them in that motherboard. Boot issues immediately told me something was wrong. A little double-checking and minor testing and I determined that the motherboard itself was bad.

If it was the PSU it would refuse to boot up at all. The usual symptoms are simple. Either the fans spin briefly and then it turns off (no boot at all, no codes on motherboard) or it will simply not turn on at all.

The random errors you're getting seem to be more indicating motherboard. Especially because of how erratic they are.

EDIT: Are these status codes where the motherboard freezes on boot up or are they just numbers you see as it boots?

That still sounds like the motherboard to me. If it had a bad capacitor it would exhibit erratic behavior like that. I mean, there is a chance that the PSU could be feeding it erratic power but I've never had one do that ever. I've dealt with a lot of PSUs, and repair them, and never came across a single one that did that. Not even the cheap Aspire PSU with a bowed circuit board.