Fans spinning up and down

Try resetting the SMC -> http://support.apple.com/kb/HT3964 Fan issues are mostly caused by SMC rather than PRAM.

If it does not work, perform an extended test with Apple Hardware Test -> Using Apple Hardware Test - Apple Support If you get an error after running the test, copy it here.

Install a Monitoring app that measure temperatures and fan speeds. I use Mac Speed Control. There are others. Maybe a bad sensor

...and you don't have your old gpu?

You do realize that not all PC cards play well, and that you read up and researched before setting on this one? even different versions and makes of the same "model" or card series differ.

AMD cards may have two BIOS, legacy and UEFI.

Thought about sending it to MacVidCards or checking?

AHT does not test GPU.

There have been issues with heatsink and paste or with upgrades - very popular to flash firmware and throw in new cpu(s)

Mac Pro 2009 upgrade running hot - MacRumors Forums

2009 Mac Pro 12-Core CPU Upgrade (Dual 3GHz Xeon X5675)

2009 8-Core Upgrade... The De-Lidded Route - MacRumors Forums

Nehalm processors with their HT can jump 20*C just launching an app or files

To see what the processor temps are, and there are many sensors and ways to monitor, you would need something more like Hardware Monitor

http://www.macupdate.com/app/mac/16609/hardware-monitor

Mac Pro 5.1 owner, make it your king of Mac with 2 D700s - MacRumors Forums

I would consider this if it is the GPU and not the processor:

http://www.macvidcards.com/store/p11/AMD_Radeon_7970_3_GB.html

HD7870 came out back around Mountain Lion and 10.8.x

http://forums.macrumors.com/showthread.php?t=1627434

http://forum.netkas.org/index.php?topic=7043.0

50C is actually on the 'warm' side, might crank up the fans to 900 rpm for now, and try to keep them - when "idle" in the 35-40C range.

http://www.macupdate.com/app/mac/23049/smcfancontrol

I set multiple profiles that have to be manually selected from the app on the menu bar to choose which, and have set them up for new defaults that set the minimum fan speeds. low (700 rpm) medium (900) etc - whatever you need or seems to help. So if you know you will be running video editing or something you could preset the fans to 1200-1500 if that helps.

I have used FanControl for 8 years, you don't and it is because Apple chose quiet over efficient.

It is a tool. Use it as such. To boost the fans a bit. My PCs run fine but fans are 900 rpm, 1200-1800 rpm and run like that for years - non-stop.

50C though is a problem, because when working, and based on Hardware Monitor, you do not want to see 75-80*C except 'briefly' and then drop down. Running cpu @ 80-85C is considered a stress test to find its threshold. That is harmful to your expensive machine.

Your gpu should also be monitored. It may be putting more heat into the system than it pushes out and is having a secondary adverse effect and why you are seeing these temps. I use an HIS card that I feel has good thermal heat management - copper cooling pipes and fans.

A finely tuned car or sports car or computer system should be treated the same way.

Even an XP941 SSD blade - no heat really, no power to run, is another way to improve performance while reducing watts and heat. Heat kills.