It could be the crank but it wasn't as common in the 99's as the 98's. Keep this in the back of your mind, but take care of other issues first to see if they solve the vibration issue.
These sleds aren't known for blowing belts at all, especially the Yamaha belts. So yes, check your clutch alignment. Also check to make sure there are no cracks running thru the sheaves that could eat away at the belt and cause it to blow. Are your clutches running hot, especially when the belt blew? They should be warm/cool to the touch at all of your smoke or bladder breaks on the trail. I've ridden with quite a few Skidoos over the years, many of them have had to change belts in front of me on the trails. I've never had to change mine in front of them, and theirs were much more expensive.
Check to make sure none of the belt fabric/stringers are wound around the crankshaft behind the primary clutch, as they can cut into the crank seal and cause an air leak that can burn down the PTO cylinder.
Clean the clutches, make sure the bushings aren't worn out, primary or secondary. Make sure the primary rollers and weights aren't sloppy or worn out. Are the plastic buttons still in place and good condition for the secondary helix. Does your secondary "float" in and out on the jackshaft by about 1/16"-1/8"? How many miles on the sled?
The bearing behind the secondary, and the bearing behind the speedometer pickup on the driveshaft below the secondary are two areas to check thoroughly. These usually aren't maintained very well and they do wear out, even to the point that the balls are gone. This could be your vibration issue. If the bearings appear good, you can carefully pick the rubber seal out and inspect closer. If the bearing looks good, and with plenty of clean grease (rare), put the seal back in, but usually you'll want to clean as much of the old dirty dried grease out and then repack with new grease, trying to push the grease thru the ball cages in 3-4 locations around the bearing. I wouldn't pack the bearing chock full, as the grease will get distributed once the bearing turns.
Service the chaincase, cleaning out any accumulated gunk, and check these bearings as well. They aren't as know for failing as much as the two on the other side, but they can fail.
Check the throttle cable adjustment, as a tight cable will trigger TORS. Once you have the throttle cable and idle speed adjusted properly, you might as well also check the oil pump cable adjustment.
You can search this site in various locations to find endless information on these maintenance and adjustment items, and SRX's in general. You can read for days. You can also download the Owners manual from Yamaha's website for free, which details all of the common operation, maintenance, and adjustment specs. If you become a VIP on this site for $15, you can contact one of the moderators that deal with the factory service manuals in the VIP section, and receive a download for that as well, then you will have even more thorough service information.
