General update:
1) Verified that soft-modding DOES NOT WORK on Kepler class GPUs (GTX6xx and later). It _looks_ like it works - the PCI device ID changes. But if you look at the GPU caps viewer, it shows the hard strap device ID. That is the ID the driver keys off, and if you don't set the full hard strap correctly, the driver will load and pretend to work, but will treat the card as a normal GeForce card and will not allow VGA passthrough to work. I have just confirmed this as the key reason why my GTX690/K2 was not working.
1.1) When you part-soft-mod, the driver will initialize the PCIe speed at 1.1 only, regardless of what the card and the bus are capable of. This is the reason why oguz286' mod was causing PCIe speed to always read v1.1 rather than higher.
In conclusion to this part - don't bother soft-modding the straps on the Keplers, it is a waste of time and will just have you chasing your tail for ages trying to figure out why everything seems to check out but doesn't work.
oguz286, if you're reading this, to get your PCIe speed above 1.1, hard-mod the 4th nibble on your 780 and you'll find it magically speeds back up. You might find performance improves in other things, too.
2) Not all GTX690s are the same. I have re-created the problem KamranB had with the modified GTX690 not working. The problem is in the mod for the 3rd nibble (if you want to mod to K2, just leave the 4th nibble resistor off). If you set that resistor to 20K, it seems to cause the SCLK output like going to the GPU to get attenuated too far and all you get is 0s, which will mean the EEPROM cannot be read. That means the card doesn't get it's BIOS initiaized and although it'll show up on the bus, it won't work. Same thing happens if you do a similar mod to oguz's VCC-SCLK resistor and use a resistor that has too low a value. You can leave the 3rd nibble resistor off but the 3rd nibble value will flap between 0xA and 0xB. I have slightly stabilized mine to the point where it is usable if you don't mind sometimes having to double-reboot by putting a 33K resistor across VCC-SCLK, but this is without any of the 3rd nibble resistors fitted. There is probably a better way to do this (maybe 40K on the original 3rd nibble resistor to replace the default 25K, or a lower value instead of 20K on the alternative location for it). I haven't experimented with this more because 1206 component soldering is not far off my manual precision limit, and 0402 is just most certainly beyond it.
GTX690 3rd nibble resistor findings
2.1) 20K on alternative location attenuates too high, eeprom becomes unreadable, card doesn't initialize, and cannot be re-flashed (don't try to re-flash it in this state, erase will work but writing will not, returning a 256-byte page programming error).
2.2) Without either 3rd nibble resistor, 15K across VCC-SCLK attenuates too high and results in the same situation as 2.1)
2.3) Without either 3rd nibble resistor, 27K across VCC-SCLK yields device ID flapping between 0x119F (
) and 0x11AF and 0x11BF. Haven't quite figured out what is going on here.
2.4) Without either 3rd nibble resistor, 33K across VCC-SCLK yields reasonable stable device ID of 0x11BF. Sometimes it flaps down to 0x11AF, but much less frequently than it would without this. Maybe a 40K resistor across those two pins would fix the problem, but I don't have any handy to try.
Anyway, the most important point here is that the documented mod for the 690 isn't universally applicable, so bear this in mind if you are modding a 690.
3) On my system the 690 is having the same dual-link mode problem as my 680. It works fine with SL-DVI modes, but causes the monitor to go to lose signal and go to sleep with a DL-DVI mode is used. Deeply bizzare and I have no explanation available for this one at all, but that does appear to be what happens. I would like to stress that this does not happen on my Quadrofied 480 (Q6000), DL-DVI modes work just fine on that. But since it is happening to me on two different cards modded in different ways, it is probably safe for others to disregard as it seems specific to my system for some unfathomable reason (but if you find the same happens to you, please do let me know, we might be able to figure out what is going on by comparing notes.
4) I have figured out the byte that controls the hierarchy ID (PCIe switch port on multi-GPU cards like the 690) in the BIOS. This would allow you to flash, say, a K5000 BIOS onto the 690, but this wouldn't work because you would need to figure out which bit in the BIOS init sets the memory size and halve it for the K5000 BIOS to work on the 690 (or a 2GB 680).
5) Because of this bizarre DL-DVI issue my 690 isn't going to be useful to me, so if somebody wants it for further experimentation, modding or just using, make me an offer in line with what they sell for on ebay. It's the Gainward model.
And now back to modding the Titan into a K6000. Need to figure out if I can pull the 4th nibble up via the SO line.