Memory:
For supported memory, you want to trying to use something from the QVL - SM provide a handy list for this, they test a lot of stuff, I would go for fastest you can afford, if you source a board with 18 dimm slots you can save a lot of money by using lots of smaller (and cheaper!) modules:
http://www.supermicro.com/support/resources/mem.cfm
Even if you won't be doing important work on the system, still try to get ECC memory, this will let you experiment with Enterprise type configurations, E.G you can system halt on an uncorrectable memory error, and monitor the rate of single bit errors - this is surprisingly useful when purchasing older used memory - as it does seem degrade over time with usage.
The only difference between registered memory and "normal" memory is the density that can be achieved, you can get much larger capacity sticks in registered form - this will be essential if you want to hit the max supported capacity of the system (most X8 series allow you to use quadrupal the amount of total memory when choosing registered dimms as opposed to using regular unbuffered dimms).
Dimm population can be complex on 2 socket boards, worth reading this:
http://www.supermicro.com/support/resources/memory/X8_DP_DIMM_population.pdf
Also worth remembering that these boards use triple channel memory - per socket!
I use 18 8GB registered ECC dimms (1333 mhz) - all pulled from exactly the same server - they are HP branded (Micron chips I think).
Power:
I think your logic is sound for the EPS power connector, though that may vary from board to board. I would not run my system on any less than a 650w PSU if it did not have a graphics card. The Corsair RM series PSUs all of have dual EPS IIRC.
Cooling:
I use really cheap Arctic Cooling freezer 2 cpu coolers, these have LGA 1366 mounting support and are ideal if your chassis does not have a height constraint - I got mine for £8 each brand new, though I think they are actually not rated for something with a TDP as high as the x5660 for example - this is not an issue for me as I have dual 120mm fans front and back to provide additional cooling
Other:
The board you are looking at is the same gen as mine - you do not get SATA3, USB3, and other modern technologies (I used addon cards to get these features) , you will also not have integrated audio which is worth thinking about if this will be your main PC - you will also not have any PCIE slots free to add these capabilities on the board you are looking at - and to my eyes your graphics card will block the SATA ports on the board being discussed too.
Try to get 2 CPUs of the same stepping - ideally from the same server.
Usage:
Until I got my TR system I used my Xeon box as my main system, that quantity of memory is extremely useful if you need a lot of VMs, or want to run DBs in memory, and 12c24t worth of CPU is more than enough power to get a lot of machines up and running - I regularly had 48 vms running on mine, or a 100GB db sat in memory.
Even though I am a huge fan of these systems - they are showing there age now - my TR system absolutely wipes the floor with the Xeon box performance wise in everyway, and even though I've got just under half the memory I used to have - increased memory bandwidth and the advent of NVME drives more than makes up for the reduced quantity of memory IMO. Power usage on these old Xeon systems is extremely high at idle compared to a modern box too - IPMI is also a great feature to have.
If you are really into tinkering and building systems - there's a lot of fun to be had with these boxes, and performance is pretty good even now, but there are also a phenomenal amount of quirks and gotchas you will hit too, they still represent the cheapest way to get a 12 core 24 thread system with more than 128gb of RAM - but IPC is quite low compared to a modern chip.
I would seriously think about whether going down this route is a good choice - as cheap as parts can be sourced, it's still not going to be that cheap in reality, and ease of use/ergonomics are very poor, and this stuff is really getting old now, so be fully prepared for quirky hardware faults (servers in many cases will have had long, hard and hot lives!).
I suppose it all hinges on: total budget + use case;
A hex core Ryzen with 32gb of RAM is probably going to be price and performance competitive, you will have access to faster disks from the get go - and still have loads of ports, modern features and a respectable 64gb memory limit, and it will all work with a cheap PSU and case that you won't have build - and all the parts will be undér warranty without the perils of auction sites, power and cooling requirements will also be much lower, and single threaded performance will be much much higher on a modern chip
Think about total CPU performance: 6 x 3.7 Ghz Ryzen cores is a lot more processing power than 6 x 2.6 Ghz 2009 era Xeon cores (by a fair amount!), plus you get faster memory and caches.
