Mac Pro (Early 2009): Upgrade Advice Requested

Hello,

I bought an early 2009 Mac Pro from OWC and the machine runs really well. However, I am looking for advice with regards to future upgrading my device. I am not an Electrical Engineer so please forgive my "amateurish" knowledge. I am, however, a Computer Science major and am hoping to milk this machine for long term usage. Since this device has the capability of DIY expansion, I am asking the community to help accomplish this goal.

The current specs are:
2 X 2.93 GHz Quad Core Intel Xeon Processors
16GB RAM 1066 MHz DDR3 ECC
NVIDIA GeForce GT 120 512 MB
750 HD I think 5500 RPM

My potential upgrades would be:
Processor: 12 Core (Dual 6 Core Unit)
RAM: 64GB short term, 128GB long term. From my reading, the motherboard "unofficially" supports 128GB.
Graphics Card: NVIDIA or AMD Radeon (Current Gen) with at least 2GB of dedicated RAM. I read Yosemite allows the GC to be upgraded.
Storage: 256 or 512 SSD for OS, 2TB for Files, 3 (or 4) TB for Backup, HD for Linux, HD for Windows.
Cooling: Maybe water cooling (if possible) or advanced cooling.

My only concern is when I upgrade any of the components, the computer will begin to overheat, causing things to become messy. I understand the newer the technology, the more efficient and less energy consumption is used. However, I live in a three story house and in a state where the Summer's are hot and want to make sure this device stays as cool as possible.

The programming I will be doing, is mostly done via XCode. I may install Windows on the device for my Visual C++ (right now I have a custom built PC for that, but may wipe it and give it to my brother). I do intend to install Red Hat to learn Linux. I may be doing some 3D programming for fun (OpenGL and Metal), which is why I am upgrading the graphics card.

Anyways, I would love to hear what your setups are and any advice you could give when upgrading the Mac Pro. (Especially the cooling situation)

Thank you!

~Lord Thalius