I feel silly. This topic was started in 2013, and I thought that the revision 3.0 was the latest in the Gigabyte UD3 revisions. The revisions 4.0 has an updated heatsink design, which helped to alleviate this issue.
Also, Jayztwocents did do a review, and recommendation, for the rev. 3.0 and 4.0, along with a $1000 AMD-based build. So, I don't feel so silly anymore.
I'll be buying ASUS when Zen comes around. I don't like my GA-990FX-UD3 rev 3.0 either. BIOS is pretty lame compared to other manufacturers' boards. I have my FX-8350 @ 4.4 on stock voltage because i'm limited by my cooler so I don't have any experience with the throttling. The board, when the power button is pressed, will turn on then off then back on again then it proceeds to post. It's repeatable on a test bench too. The board also has issues with booting from USB. no idea why.
I normally recommend Gigabyte and Asus over any other brand. For example, if given the option of the MSI versus Gigabyte.....Gigabyte. I have been burned one too many times by MSI. My Last AMD board was an ASUS Crossfire V Formula board with I think a Rev 1 or 2. It worked OK until the onboard NIC and Audio completely failed. When I sold that board I had to include a Gigabit NIC with it in order to sell it. It is too bad AM3+ is not seen in Mini-ITX boards. I rather like Gigabyte's Z97 Mini-ITX boards.
Ok so you removed the vrm cooler and complain that your board overheats? Then you attach some fan over the bare copper in hopes that will remove heat? Even the other pictures you provided are confusing with how you have your cooling setup on your board. I don't get it. I have that exact same board with no problems.
He removed the stock heatsink and replaced it with an aftermarket heatsink, which, if you are familiar with heatsinks, was made by Enzotech - they make pretty good quality stuff. He added a fan after swapping the heatsink did not to the trick.
The Revision 3.0 did not have the best heatsink design. Revision 4.0 fixed this, for the most part. His problem probably occured because he was water-cooling, and his VRM lacked proper airflow. (His outtake also had the radiator mounted on it - bad airflow for the VRM.)