Hello Scott,
I've actually decided to go via PCIE for both the SSD and M.2.
1. The M.2 will be plugged into one of the motherboards PCIE2 x 16 slots via the following adapter:
Angelbird Wings PX1 PCIe x4 M.2 Adapter
...the adapter is necessary when using the Samsung 950 M.2:
...as the 950 is notorious for its drop in performance when thermal throttling.
Using the M.2 in the PCIE2 x 16 slot should give me about 1500 MB / sec sequential read performance (compared to the maximum of 2500 MB / sec if plugged into a PCIE3 x 16 slot) as well as 1000 MB / sec sequential write preformance ((compared to the maximum of 1500 MB / sec if plugged into a PCIE3 x 16 slot).
2. The other PCIE2 x 16 slot will be populated by a graphics card such as the Nvidia GTX 1080 (I've seen multiple articles detailing that the drop in performance between plugging in a graphics card into a PCIE2 x 16 vs a PCIE3 x 16 as being a difference in a few percentage points, ex 1 - 3%).
3. I plan on purchasing an SSD (as secondary storage) and plugging in the SSD into the sole PCIE2 x8 on the motherboard via the following adapter:
The SSD in question is the Samsung 850 Pro (likely a 2TB version).
With the adapter, I don't see how I will be limited (plus the adapter comes with a secondary SATA III port - which could be useful for another drive in the future).
4. The remaining PCIE x8 (generation 1.0 not 2.0 like the port from point 3) will be used for a USB3 PCIE express adapter such as the following:
https://www.amazon.com/dp/B00FPIMJEW/ref=psdc_229185_t3_B01C59TB0I
5. As for RAM, I can almost confirm that the following 48 GB sticks should work:
http://www.newegg.com/Product/Product.aspx?Item=9SIA8H53HD5595
Buying 2 pairs (each pair consists of 3 - 8 GB sticks) should push me to 48 GB and spec wise, they match up perfectly with my pre-existing RAM.
6. CPU will be upgraded to a X5690 (used go for around $200.00)
Nelson