Why would you need GPUs in a server for transcoding? You can add the M.2 on a PCIe card, so I'm gonna ignore that requirement to give you best value.
Either way...
CPU: Dual E5-2667s? Your choice there, really.
Mobo: Gigabyte GA-7PESH2 - has 16 RAM slots, dual CPU sockets, 2 10gigabit ports + a dedicated IPMI NIC, plus two PCIE ports for a GPU, 2 onboard SAS2 sockets (up to 8 drives each). https://www.theitmart.com/GA-7PESH2-GIGABYTE-Intel-Rev10-LGA2011-E-ATX-Server-Motherboard
RAM: 4-8x 8GB ECC DDR3; pick it up off ebay.
Case: 4U Rosewill w/ 15 drive bays: https://www.amazon.com/gp/product/B0091IZ1ZG/
PSU: Whatever you want, needs to have dual EPS power and a 24pin plus whatever you need for your GPU(s). (Though I guess you could use an EPS splitter but I really wouldn't recommend it)