First off: "Typhon Mark II", "Typhon II", "Typhon 2", and "Typhon-R".
These are too generic and different to be recognizable as a *variant*. "Typhon-R" fits with existing recognizable conventions such as the Prometheus-R(etrofit), but "retrofit" means to add stuff AFTER something is manufactured. TrashMan's Typhon variant needs a name that stands out and shows that it's your average Typhon, just different.
Besides, the variant needs to be named something other than "Typhon 2" as someone else might want to make a Typhon 2 that is a larger step ahead of the existing Typhon than what TrashMan has created...so...here's a nice catchy one I've got for you people.
"Typhon-Ra"
I like this a LOT. It sounds cool and Vasudan-y, with a nice ring to it too. Picture it in a command transmission: "The GVD Sphinx*, a Typhon-Ra class destroyer is headed..." --- DEFINITELY fits well, doesn't it? Would kinda sound silly for Command to SAY "Mark II", "2", or "R" in a transmission. Of the three, I recommend this one hands-down.
Oh, and I can't say this is a problem really, but Raa might want his smooooooth Original Typhon to be called Typhon-Ra or something too. So IF TrashMan uses "Typhon-Ra", Raa can call his smooth one "Typhon-Raa" LOL

*GVD Sphinx is just the first example that came to mind. It means nothing.