I feel your frustration. I have a 2015 STX-DX 141" and I too have the exact same thing. I bought the sled new and after 2 rides (430km) the sides of my track looked terrible. I couldn't align it, the front side is far left in the drive sprockets and the back side predominantly to the right in order to keep it from rubbing on the left up in the tunnel. It is clearly on an angle. Based on my findings after measuring everything X pattern, sprockets, etc. I don't see how it will ever work, which is likely why there is a lot of discussion on this topic. Based on my findings the track is allowed to float side to side by about 3/8" before the slider rails will retain it. Normal right, right. The problem lies in the tunnel since the track is 15" wide and the tunnel is only 15.5" wide. The bolt heads and rivets on each side chew up an additional 1/4" leaving only 1/8" clearance on each side of the track. Personally, I think it is bad design, having only 1/8" clearance on either side of a large track to float before running into the backs of rivets and bolt heads. It's clear to me that no matter where you set the track, it's going to destroy the edges of itself as soon as you turn a corner.
Yamaha corporate responded saying all of their Vipers rub and in fact, they have not seen one unit that does not have some "slight" rubbing. I was told to just get back out and enjoy my sled and the this is perfectly normal. The dealer didn't even try to align the track. What he did do is spent a lot of time with a raiser blade cleaning up the edges and he used something black to cover up the white threads... 1 month later, I picked up the sled and still have the same problem going into next season. For the record, I love Yamaha products but after this experience, I will never buy a Yamaha product again.