I can only help with one of those. The new shroud is currently not being shipped out with new cards, so everything in stock currently will have the old shroud. I am sure EVGA will make an announcement when new units will start to ship with the new shrouds. I replaced the fan on my radiator with 2 x Corsair SP120 PWM, and then control them from my motherboard. I can say that I run them at 1600rpm and it runs much cooler, but it is certainly louder than the reference fan. I am happy with the trade-offs however.
 
EDIT: The review you linked to is remarking that the VRMs are hot, and look like they're not watercooled, not the VRAM. VRMs are voltage regulation modules, they deal with all electricity supplied to the rest of the card and most people will say that higher temperatures will mean lower efficiency and less stringent control on the voltages supplied, which can theoretically lead to instability. I would say that 77C is well within standard operating specifications for these components, but you have to bear in mind that the temperatures recorded via thermal imaging are only indicative of the surface temperature of the back plate. The actual component temperature will be higher. I have heard people estimate that component temperature is generally around 10C higher than a heatsink/plates surface temperature, but it really depends upon thermal conductivity properties, which would require some testing to calculate. I can say that I fix the blower on my hybrid card to 45% at standard voltages, and it can run for days without any excessive hot points or instabilities, but I do not have a thermal camera to offer any comparison. I have thought about buying one, maybe next year, lol.
 
EDIT EDIT: http://www.guru3d.com/articles_pages/gigabyte_geforce_gtx_980_ti_extreme_gaming_waterforce_review,37.html shows you how much hotter the VRMs get when you apply 87mV extra voltage to the GPU. The VRMs light up in the high 80s, and that's through the backplate. These are still within accepted operating parameters though.

Gentle Typhoon on Hybrid will work excellent, special if you have 1850 RPM version.
Silence and lot of air. 

Personally, I would go with your suggestion of installing the hybrid rads in 1 and 4. The Air 540 case has whopping big holes in the bottom of it, so you ideally want a slight positive pressure in the case to keep dust out (i.e. more air coming in to the case than coming out). Do remember however that an unrestricted fan will move more air than a fan mounted to a radiator, even one designed for static pressure. Also bear in mind that the 2 GPU's have attached blowers that exhaust air out of the case as well, albeit only a relatively small amount since the speeds are slow on the hybrids.
 
Of course for most people this is probably not that important, but I am overconscientious when it comes to temperatures.
 
EDIT: Forgot to mention that if your radiators are mounted vertically (which they would be in positions 1 and 4), the hoses should be at the bottom. This means that any air in the system will sit at the top of the radiator (the highest point) and no longer be drawn in to the pump, which can create an annoying gurgling sound (and even increased temperatures in extreme cases). Some people have issues with this, some don't, so it is worth installing this way around if you have the space just to avoid potential issues entirely.
 
EDIT EDIT: Also remember that you are right that you would want the radiator installed in position 1 to be set up as intake, but remember that this will mean that ~30% of the air coming in to the case will then be effectively preheated, so you may need to increase the other intake  fan speeds to maintain a low temperature inside your case, and you *may* find a very slight increase in your cpu temps, although this should be relatively marginal. You might also find that the hybrid installed in to position 4 will run at a slightly higher temp as well, for the same reason.
 
Installing a radiator as an intake is not ideal, but in your case, you don't have much of an alternative, unless you want to either buy a new case, or go full custom, which kind of defeats the point in buying the hybrids. I doubt you'll find the temps that terrible to be honest, but bear in mind what I said earlier about my obsession with temperatures, lol.