Low, unplayable fps after hardware upgrade

The R9290 should run the graphics fine, in mostly ultras so I have to assume there is something bottlenecking your CPU or a driver issue.

First thing I would try is make sure all drivers are up to date...since you recently built it, they should...but go back and make sure your drivers are the latest available.

Second would be to download Microsoft Process Explorer

This should show you if you have a background process hogging all your cpu when trying to play the game or if there is something else going on.  I would also download Afterburner and speedfan or equivalent programs to see if you have an issue with heat, because the game does stress components a good bit(not too likely). 

Third thing would be to double check your powersupply rating and make sure you have enough to run everything in your system.....you should, since the I5 is supposed to take less than the AMD chips, but the 290 can be a bit of a PSU hog depending on which one you got.  This is just a cover your ( ! ) , check.....

I assume you already installed a fresh windows install after switching motherboard+cpu?

Correct, Fresh install on SSD, only a few weeks old.

As far as drivers, the video card is auto updated via AMD gaming evolved. I am not sure about CPU, I have never updated CPU drivers to be honest. What else would I have to update?

My Power supply is a TX750, unless something is wrong with it, I don't think it is the problem. I have no issues in any other games, which is why this has me stumped. 

I originally had the game installed on my D drive but have since moved it to the SSD with the problem persisting.

I will update with any findings with process explorer! I have also left HWmonitor up with no temp. scares but as I said, I can't even get past the menu screen so I can't imagine the GPU going from zero-max temp just from opening the game, before the menu loads.

I'm not too sure how to use the process manager but it doesn't look like I am maxing out during idle and will see what happens when I run the game and update.

Okay, while game is off my cpu bounces from 20-30%, with game running it sits at 98-100% on menu screen, Ram is at 3.4(about 1/4 of usage), and GPU is at 2.15-3.15%, at menu screen.  I am not sure how I can go into more detail here, to be helpful. 

The changed factor is your MB and CPU....so that makes it tough.

Did you make sure your BIOS is the newest available?

Did you overclock your new processor?  Are your ram speeds set correctly in BIOS to accommodate the motherboard?  If all that is checked, it may be hardware.  

Hardware wise, did you re-silicon the new CPU to the new MB?  Sometimes the heat production is much more unless you re-apply the cooling agent.  Are you using a different CPU cooler than before?

The issue appears to be the CPU. A quad-core i5 normally has issues with the game. My i7-4790k runs it just fine. This game demands CPUs with eight threads / cores to run properly. You were running the game fine before because you had an eight-core AMD CPU. I would suggest returning the i5-4690k and getting the i7-4790k. It sucks to pay a price premium for a high-end CPU to play this game, but in the long run, it will be worth it.

No it doesn't require 8 cores to run the game...

Mine is running just fine with
AMD Phenom II Black 3.5ghz quad core
12 gigs ram
AMD R9 290X MSI Lightning
2x 1tb Hard drives

And previously I had both one and two AMD hd6950s running the game in graphics fine too, so while an I7 would be nice, it shouldn't be required...unless you are somehow saying my several year old PhenomII is better than a newer I5....

Some setting or driver is causing the issue, it isn't the power of the chip.

It seems this was exactly my issue. No other game seemed affected by this at all. The process in question was "xboxlivestat.exe" or something similar, I will update it after I reboot and have to kill it again.

I'm guessing it is something being ran because I have a wireless xb receiver hooked up to my PC but it continues to work after the process is killed, so I will figure out how to get rid of it!

Thank you everyone for your input/help/idea bouncing! I did double check everything in bios(mostly auto settings/factory), uninstalled/re installed programs such as the game and virus programs, and rolled back a few times. UGh..

that is ...

Xbox Live Stat .exe

Do you have any program that mines or watches your stats for your Xbox account??  That doesn't look like something I would see with just a wireless controller....I could be wrong though...have been before and will be again.

I've got no games that are (originally) GFWL, which is what I thought it would be from, Not sure what other games would be subject to such a thing :P 

The path for said process is : "C:\Program Files\Microsoft Xbox 360 Accessories\XBoxStat.exe"

The program name is "Microsoft Xbox 360 Accessories Status" and I believe it was auto installed when I plugged in my authentic MS Xbox 360 controllers wireless adapter.

It is def. the culprit and after scouring the web, I have found that this process can actually mess with your hard drive, which I believe I was a victim of also, My secondary hard drive has been making an odd noise, like it is working hard all of the time, as soon as this process is killed, it stops! 

It is not malware, I have uninstalled and re installed the program via the wireless adapter and the problem persists!

Since I need the XB360 driver, I have left it and the driver installed on the PC but I have disabled the "XBoxStat.exe" on startup via MSCONFIG.

After rebooting, I can run dragon age: I on ultra, with no hiccups. I have also seen a boost in other games that I wasn't noticing any problems in. BF went from an average of 70-120FPS with a max of 140 to an average of 120-150 with a max of 200! Dayz also runs smoother but still has issue with cities but it's way more playable than it was!