Just ride it and get used to it. Do some searched on mods and decide from there what you want to do. A good place to check out is Totaly Yamaha 4stroke forum (TY4Stroke forum), tons of great info on the Nytro there as well as all other yamaha 4 strokes. The mod you choose will depend on what syle of riding you do and what you want out of the sled. I don't have a Nytro but i have several buddies I ride with that do. They absolutly love the nytro. I am seriously looking at one in the future. It's all personnal preferance and opinion. I have over 15,000 trouble free miles on my RX1 and it is still running strong. The RX1 has had some issues compared to the newer sleds but I like it and thats all that matters.
The nytro can't be that bad of a sled, there are tons of them out there. As far as the oil goes, if it is still on warrenty i would check with the dealer to see if you have to use yamaha oil for warranty purposes. If not lots of guys using the mobile1 0w40 eurpoean formula.
As for the Viper, it's not as bulletproof as it is made out to be. Check out the Viper section on the ty4stroke forum. Again I don't own one it's just what I am reading. All first year sleds, quads , bikes, cars....... have there issues. It's tough to find all the issues with only a few test models out there. Its when you start running hundreds or thousands is when you start to find the issues. Hopefuly Yamaha will fix these issues on next years model. I would love to have a Viper but like the OP said it just not in the cards for me right now so I will do the same an buy a used Nytro.