Just can't see the reason why worth to do this.
A used 2009 model (4,1) just around $400 (single processor), $600 (dual processor), which effectively the same machine as the 2012 model (5,1) after firmware flashing.
And you still have around $1000 to upgrade (SSD, GPU, CPU, RAM, USB 3.0...). This can gives you a very good cMP with $1500.
To build another one.....
Case $500 (NEW)
Processor cage $25 (NEW)
Front Fan $45 (NEW)
Rear Fan $40 (NEW)
PCIe Fan $25 (NEW)
Power cord $20 (NEW)
PCIe card bracket $10 (NEW)
PCIe fence power cover x3 $60 (assume only graphic card installed in Slot 1, so 3 cover required)
Memory $70 (assume using 3rd party RAM to improve the cost to performance ratio)
CPU tray $650 (NEW, dual processor model)
CPU tray support plate $20 (NEW)
logic board $330 (NEW)
Super drive $50 (NEW)
Optical drive cage $10 (NEW)
CPU $200 (assume using used CPU to improve cost to performance ratio)
Heatsink A $180 (NEW)
Heatsink B $240 (NEW)
PSU $290 (NEW)
PSU cable cover $30 (NEW)
GPU $150 (Assume get a used GPU and flash it by yourself to improve cost to performance ratio)
Airport card $50 (assume you get a 802.11ac card)
HDD tray x4 $120 (or you can go for SSD adaptor straight away, Stock Apple SSD tray $45 each NEW)
Keyboard, mouse, thermal paste, cables.... $100
Not sure if I miss anything else, however, up to this point, this "NEW" build already cost $3200
If I really want to build something from scratch now, sure I will go for the Hackintosh, which can gives me a 6700K + 980Ti, PCIe SSD......with much lower cost.