UPDATE:
I managed to update the UBoot after verifying that my SAM460ex is a 50 baseclock. Thanks to Jabirulo, in a different forum, for pointing out that I needed to make the utility executable.
Now I have to wait for my son to give a me hand swapping the gfx card back in again. My son is in the business of building gaming PC's, so is very handy with hardware upgrades.
I'll let you know how it goes later. Fingers crossed.
UPDATE July 5th, 2015 - 4:49 PM Pacific Time
After completing UBoot update, we put the VisionTek HD7750 gfx card, but again no luck. We tried connecting to the monitor with HDMI, DVI and VGA, with no results in either case.
There is no signal from the computer to the monitor.
The 7750 card was tested again in a PC and it works fine.
Any other suggestions?