Wiseco piston, Stage 3 camshaft, Harley Dyna muffler....a bit of work to the head to improve the ports, Kawasaki 25T front pulley, 140/90-15 rear tire.  (Double Kawasaki pulley mod that will lower the rpm at speed).

My bike has the above mods and a double Kawasaki pulley mod with an 18" rear wheel and tire, and I can cruise at 70mph at 4,000 rpm all day long.  It reaches 80mph quickly and easily.....but the light weight and altered geometry of the Cafe' conversion that makes it such a joy in the corners begins to make it a bit skittish at high speeds.  I have gone 101.1 mph twice (GPS speedometer with accurate reading)......it just doesn't want to go any faster than that and the steering is really wiggly at that speed.

I think cruising at 85mph for extended periods on a Savage is a bit optimistic, as the engine goes through a lot of oil when you keep engine speeds at high rpm for extended periods - but I think 75mph is certainly obtainable with about $2,000 worth of engine/drive train parts!

The 2 things I've been reading the most is a chain conversion and performance cams that make the biggest impact. I was thinking of chain converting it with some gs550 sprockets and chain. If I feel like I need more, I can get more by upgrading my cam. I've played with my carb already. The jetting seems pretty good. It just feels like the bike has so much untapped potential up in the top end. Good point on weather conditions. I'll pay more attention to my morning commute and how it runs compared to 90 degree Texas heat when I ride on the weekends.

Of all the bikes I own, the S40 is the one that I have no interest in riding above 65-70. The sweet spot is well below that speed. Wanna go fast, you’re on the wrong bike. Doesn’t have the brakes or suspension for high speed. And I say that, with optimized brakes (320mm rotor and R1 caliper) and suspension.  

If the bike won't do what you want it to, you may need to adjust and accept it and its limitations. I have. It's just such a cool around town ride that I accept its highway limitations and look for ways to avoid the slab.

This one does 85mph and the motor was never opened. Just drop a lot of weight, install a 160 main jet with a proper intake and pipe, and convert to chain with a better highway ratio.

Mine cruises at 85+ pretty easily.  Noisy, but no other worries.  Pinned it will climb and sustain 95-98, but its a little shaky. Its got to be on a downhill grade to get over 100, just wont do it on its own.  My speedo is GPS, so it ought to be accurate.

Stock motor, belt and pulley's,
5 speed gearbox
aftermarket Keihin PWK38 carb with pod filter,
Dunstal type pipe
18 wheel on back
Im at about 200lbs naked, but I ride with clothes usually.

I've had two Savages, an old 4-speed and my current 2016.  Both of them would run up to 80+ pretty much stock (a little jetting work, but otherwise stock).  Just as Dave said, they will run up to 80 pretty quick, but from that point on they start to struggle.  I personally believe the rate of acceleration drops dramatically past 80 mph due to the single-cylinder engine.

An average 650 twin has much better acceleration above 80 mph, and a 650 inline 4 even better.  That big single cylinder spends too much time between power strokes to overcome the aerodynamic drag.

That being said, let's address your issue with acceleration at higher speeds.  Keep in mind that due to aerodynamic drag the horsepower required to power a vehicle increases by the cube of its speed.  The stock Savage makes about 30 to 31 HP, but it starts to go flat at 4500 rpm (65 mph) and signs off right about 5500 rpm.  With stock wheels & gearing, the engine is running 5600 rpm @ 85 mph.  So right at the point where you want the power building to overcome the exponentially increasing aerodynamic drag, it's flatlined.  And when you approach the desired speed (85 MPH), power is declining.

You can extend the power band by installing an inexpensive camshaft along with modifying your stock airbox and muffler, and rejetting the carburetor to suit the engine mods.  The cam will set you back about $165. The airbox mods are free (keep the stock filter, it flows well enough to support significantly more horsepower).  The muffler mods are inexpensive as long as you have a decent set of tools and the skills to use them.  The jets will probably set you back $25 or less.

Those modifications will increase your power by about 3 HP and 4 ft-lbs. Of more significance, your powerband will be extended all the way to 6500 rpm.  

After performing these relatively simple mods, when you reach 85 MPH (5600 rpm) the engine will be in the sweet spot and still have another 900 rpm of reserve to maintain your momentum.

Don't think you will be riding a Top Fuel dragbike.  It's still gonna struggle past 85.  It's that single-cylinder thing.  There's 580 degrees of crankshaft rotation between powerstrokes.  So 75% of the time, it's not making power.

That brings to mind an interesting topic, the flywheel.  Some of us are using lightened flywheels.  I have a very light flywheel on my bike and I believe its probably beneficial to my quest for faster acceleration, at least in the lower gears.  But I have a suspicion that once my speed starts to get past a certain point (maybe 70 to 80 MPH), the absence of flywheel mass starts to work against me.  Flywheels are primarily intended to store energy.  You get it rotating and it doesn't want to stop.  So during that 75% of the time that the engine isn't on a power stroke, the flywheel inertia keeps things moving forward.  That helps to maintain higher speeds, and might possibly aid in acceleration at higher speeds because you won't lose as much ground between power strokes.  Since you want to improve your bike's ability to cruise and pass at high speed, I would leave the flywheel as-is.

You could reduce your final drive ratio by installing a smaller rear pulley, a larger front pulley, or both, but it seems to me you aren't looking for a more relaxed high speed cruise but rather faster acceleration at high speeds, so I suspect engine mods are more suitable for your situation.

If you are interested in the cam and simple airbox and muffler mods, LMK and I will post the links.