I just put mine in last night so it is still fresh in my mind. When you look up under the back of the seat you will see the heat exchanger that goes across the back of the sled, you also have the two long ones that run to the front of the tunnel, and yes they are above the windows in the track. In between the rear heat exchanger and the long ones there is a little ramp type thing on each side that is fastened on with four rivets each. You take out the two back seat bolts and prop up the back of the seat, then you drill out those four rivets that are holding on the ramp shape thingys. You then have to pound the remainder of the rivets up through from the bottom and fish them out from under the seat. Then take the two new longer protectors and fasten them using the two front holes from the ones you just took off. Then you drill the other holes for the remaining rivets, this is where it gets tricky because you are actually drilling into a little tab on the bottom of the rear heat exhanger!!! I made my own drill bit stop and clamped it on the bit so that I would not go too deep and get into the coolant reservoir.
The protectors have been discontinued by just about every company but you can still find them on ebay and such. I just did a search and found these ones on ebay. Go to ebay and in the search box type in item # 300489769378 and you will find some yamaha protectors. The ones I got were made by bender but were the same exact thing, only problem was mine did not include all the rivets so I just put two in the front holes and two in the back and didn't worry about the middle ones. Also the ones I got had really good directions with them which I still have so if you find a set and need a copy of the directions as to how they go on let me know.