From what I understand, (and I'm not a viper owner), the ecu is a CAT piece, and not the same as the Nytro ecu. This could explain a calibration issue, but if the sled is getting too hot to restart, there's another issue there. Even though the temp rises after shut down, it shouldn't rise enough to over heat. If this is a problem, I'd be looking at ways to increase the cooling ability if the system, and ways to shed the under hood heat from exhaust, etc.
Also, this sled is built in the us, not Japan like other Yamaha models. I'm not certain that it would be built/shipped with 100% antifreeze, but anything is possible..
On my sleds, I've gotten rid of the green antifreeze, and I run BE-Cool's antifreeze, which I use in all my cars. It will cure a marginal hot asked issue with no problems, and does not get diluted. By far the best coolant I've ever used. Pm me if anyone wants some, I carry it at my shop.