I was talking to the raw binary code hex editor view, but you should be able to verify the exact location of the bytes you need to change using nvbios dumps.
Loss of fan control and video outputs is exactly the reason why I suggested modifying into a K5000 rather than K2, since the K5000 is supported for all of the same VGPU functionality as a K2, and as I mentioned before I ran a 4GB GTX680 with a K5000 BIOS on it with no ill effects.
Did you modify the device id hierarchy IDs on the primary K2 BIOS to make it work on a 680? nvflash shouldn't have even allowed you to flash the BIOS onto the card if you hadn't adjusted that.
Did you remember to rebuild the BIOS checksum using KBT after you modified the BIOS? If the checksum is invalid, the card won't work with similar symptoms to what you are describing.
For normal PCI passthrough, all the modified cards I tried work fine - over time I have used 450, 470, 480, 670, 680, 690 and currently 780Ti. If normal PCI passthrough doesn't work, the modified BIOS is broken.
I wouldn't expect the EEPROM to expire in fewer than 1000 writes. I did kill the EEPROM on my sacrificial GTX450 way back when I was still researching what strap bits do, but that involved trying to go through many, many permutations of strap bits in an automated way (nvflash the straps on a 450 running as a secondary card, reboot, capture lspci -vvvv, repeat...) and eventually it gave up.
You might want to investigate further using a cheap GTX470 or GTX480 card. No hardware modification required, it's all controlled by the soft straps. Get a Q5000 or Q6000 BIOS, make sure the device ID strap bits are suitably set for the GeForce card to result in the equivalent Quadro, modify the RAM configuration block to adjust the size from 6GB to 1.5GB (or 5GB to 1.25GB in case of the Q5000), fix the checksum with KBT, flash that on, and see how you get on. The Fermi cards didn't have UEFI headers and crypto signatures, so with a modified BIOS on those you won't be getting thwarted if the newer drivers check the BIOS' crypto signatures. A high end Fermi card is probably a much better candidate for exprimentation with this kind of thing than the Kepler cards. And of course they are much cheaper nowdays, so not as big a loss of you break one. Quadro 5000 and Quadro 6000 are both supported for ESXi VSGA, so in theory the functionality is there. I remember reading about a demo system somebody put together, running 6 gaming seats (Borderlands at 800x600@25fps) on a single Q6000. Obviously you won't get that many with 1/4 of the RAM on a 480, but it should be sufficient for experimental purposes. Whether Xen actually supports the older Fermi cards, I don't know, but ESXi definitely did.
On a separate note, if you want VSGA/VGPU type functionality, there are other ways to achieve something equivalent. Run VMware Player 5 (6 has somewhat broken 3D acceleration in my experience), and once you get 3D accelerated VMware drivers installed, also install Kainy. That will do realtime video compression (CPU based, sadly, so you'll need plenty of CPU) and allow you to output it to a Kainy client (which exists for Windows, Linux and Android). It effectively gives you the equivalent capability stack to VSGA/VGPU and Nvidia Shield. And best of all, you don't even have to use an Nvidia card. Not as performant as VSGA/VGPU, but when I tested it as a proof of concept it worked usably well.