That's a very specific diagnosis.  How do you know it's the primary gear?  Previous post was about tire clearance being your noise on decel.  

The 140/90 tire fits fine.  Many Savage owners run 140/90.

For the $1200 you paid, you can expect some issues.  What's your mileage?  I doubt it's a bad primary gear.

Mine has a slight whine sometimes I'm pretty sure it's the belt might be your case to check the belt is riding mostly even on pulley and check belt tension and maybe even clean the belt oand pulleys debris.

If its normal noise then so be it, not gonna mess with it. The tire height really isn't the trouble its the width on the right side. Its stupid close with this Shinko tire. Maybe the Shinko is wider than other tires the same size. The bolts sure looked factory to me. I talked with the people I bought it from and they simply had it to the dealer for service. Dealer put the heavy oil in and changed the tires!  Before I opened up the sissy bar 1/4 inch the fender was 1mm from the tires edge and the entire bolt heads were into the tire when the suspension moved. I'm dam lucky I only drove it a few miles with the shocks all the way down. I'll check out the belt next, I have severe arthritis gonna take a break for a few days my hands swollen badly from yesterdays marathon LOL.

Your rear tire rub is very interesting.  Is there a chance that your rear wheel is off-center?  There are four spacers associated with the rear wheel.  Two are exposed and two are inside the assembly.  The right-side spacer is considerably thinner than the left-side spacer.  Is there a chance that these spacers could have been mixed up or left out, resulting in your rear wheel shifting to the right?  The right-side spacer should be 22.3mm thick.

Regarding your "Primary Noise".  The early models had a primary drive ratio of 36/68 while the late models have a primary ratio of 37/67.  It is possible to mix them up (difficult but possible).  They will engage almost all the way, then nut will do the rest.  I tried to fit them up just to see.  It would be ugly, and I can imagine the noise would be impressive.  It's easy to check.

You should have 37/67.  Because you only make noise during deceleration, I suspect your issue is with the final drive, not the primary.  But I haven't had the benefit of hearing the noise.

Don't overlook Paul's comment regarding the pulley cover.  It's easy to screw up.  Easy to check too.  

There are thick grommets and thin grommets.  The thick ones go on the inside, the thin ones go on the outside.  If you reverse them it rubs on the pulley.  Makes a lot of noise.  To check, just remove the cover and take a short ride.  Of course, you need to be careful not to get your pants tangled up in the pulley.

After thinking about this over night I think you may have something on the spacing on the rear rim. I noticed the belt hangs to the outside of the rear pulley too. Do you know where I can find a layout diagram of what should be where? Right now the short spacer is on the right side and the longer on the left but you mention a internal spacer. Maybe something funky going on in there. I was surprised to find the tire jamming up against the bolts but so far I can't find any logic in it except the oversize tire.

I also searched online and found quite a few people on this site and others complaining about the exact same whine noise. Heavy whine like a old Jeep only on decel. One post claimed switching to Rotella stopped most of it. They didn't mention which Rotella they used though 4 5 or 6. Honestly next time I buy a bike its going for a extended ride! I got a great deal on it but not having to worry on blowing the rear tire gears etc just aint makin me jump for joy. Makes me very uneasy to drive this after seeing that tire chopped up like that.