new build plan.

Solution
The build I posted was only to show you that you could get a I5/GTX 980ti for a good price, I dont expect you to follow that build lol. The reason I went with the 500gb SSD is because theres a very high chance I will need to remove the HDD cages for the PSU and also modify the case to house the H100i and I wanted plenty of room for OS and games. If I can fit everything and a HDD then i'll just add in a 1 or 2tb WD Black for storage. Ok so going back to your build I still would stick with build A, that Xeon should last for quite awhile and when DX12 is released it should help utilize HT much more effectively and be just as good as that X99 build. Personally I only overclock to fix "bottlenecking" issues but depending on which programs...

gaming is going to be a secondary for me (just a way to unwind on the weekends) this is going to be my college rig, so a lot of multitaskings, some animations, coding, bit of rendering, some light emulations. ill only be using one 1080p monitor which is going to be at 60hz (and might possibly hook up my old little monitor if i can) just for some easier multitasking. don't know if i can hook up 2 monitors at once, one through a normal mini display or hdmi, and the other through DVI or whatever it is.
i will be doing a lot of computing so a more beefy GPU would come in handy to powerhouse it, my main priority is getting a good, up to date processor, motherboard and ram, which is a bigger pain in the ass to upgrade than a GPU. and while i would love to have a small form factor pc, like the one your planning on making, i need a ATX X99 board for the processor.
i might OC a little bit just for a bit of a boost when i need it but won't push it up to fast till i get a better cooler once i can afford one.
and just wondering, why are you getting a 500gb SSD? why not a 120gb SSD boot drive for like, 55 bucks and then get a 3TB storage drive? just seems like not a lot of storage for a gaming pc unless its just going to be a LAN party pc or if your using a mother pc for your main gaming and just transferring over the files. (I never really got onto the SSD hype train so i don't get the point of them to much)
 
The build I posted was only to show you that you could get a I5/GTX 980ti for a good price, I dont expect you to follow that build lol. The reason I went with the 500gb SSD is because theres a very high chance I will need to remove the HDD cages for the PSU and also modify the case to house the H100i and I wanted plenty of room for OS and games. If I can fit everything and a HDD then i'll just add in a 1 or 2tb WD Black for storage. Ok so going back to your build I still would stick with build A, that Xeon should last for quite awhile and when DX12 is released it should help utilize HT much more effectively and be just as good as that X99 build. Personally I only overclock to fix "bottlenecking" issues but depending on which programs you use you could probably see a significant increase in performance, so then the X99 might be better after overclocking. I still think the Xeon is a excellent choice since it will run much cooler since its using less power and doesnt have a iGPU and the savings go towards the SSD/HDD combo.
 
Solution
ah, i see your point. another issue i have is it being semi future proof, the X99 seems to be the way thing will be going, and id like to not have to replace a lot in the next four years ( tearing down my computer in the middle of college just seems messy, not to mention ill have a very limited income) so for me the benefits just seems to go towards the X99, that way i get the much higher speed of the DDR4, and will only have to upgrade the GPU once i need to instead of the CPU, MOBO, and RAM. ill definitely consider what you said though and probably tweak my option A around to see if i want to go with it.
 

if i can ill definitely get one of those sky lake processors but i doubt ill have time to wait for it, I've got to have this thing built by august 10th so not a lot of time to wait for new parts to come out