From experience, I would recommend against the X8SIA-F unless you have a specific need for that many PCIe slots, as it uses a PCIe bridge. Bridge chips can occasionally cause compatibility and stability issues. I personally had an issue with an X8SIA-F where an SAS controller behaved erratically in a bridged slot but the problems went away when moved to a direct-connected slot. Plus, just in general, you have one more chip on the board, so one more thing drawing power, and one more point of failure. The X8SIL-F has two x8 and one x4 slot, which should be enough to support a ton of drives, and the X8SI6 has a really nice controller on it already plus a few extra PCIe slots and more memory slots than the X8SIL (not that it matters with unbuffered DIMMs).
As for hardware, I highly recommend the Xeon X34x0 chips (I have an X3440). If you use a Core i3/5/7, you lose ECC capability, so you might as well just get a good non-ECC board if you go that route, unless you really really need the IPMI controller.
The Kingston KVR1333D3E9SK2/4G RAM mentioned in the DIY Server article is a very popular choice and is known to work well with the Supermicro boards (as well as Intel boards). I'd recommend going with the 8G version of that kit though, which I think is part #KVR1333D3E9SK2/8G. Because these are unbuffered DIMMs, you can only use a maximum of 4 of them on any of these boards, so the 8G kits will allow you to expand to 16GB.