IF they are the original carbs for your 90S, then the mixture screw should be downstream of the throttle slide - this means that it is a FUEL mixture screw, as opposed to an air mixture screw. If it is in the intake bell (on the air cleaner side of the slide), then it's the other way around. The fuel mixture screw meters the fuel supplied by the idle jet - so, it is backwards from the way that an air adjusting screw (as used on Bing CVs) would work. IOW, as you turn the screw IN, you are DEcreasing the amount of fuel being supplied while the air supply remains constant: IN=leaner.

BUT - running up a hill on one cylinder doesn't have much to do with idle mixture settings.

"Middle notch" - there are four notches, so do you mean the second or third? I don't think I've ever set up an R90S with anything but the third notch - it might not be the technical ideal, but it will certainly get you close.

Synching - do your carbs have take-off ports? If so, use a manometer of some type. I personally prefer mercury columns that respond to each individual cylinder (carb sticks) - but, a differential gauge ($4 carb balancer) will work. If no port, try this quick and dirty method that gets them damn close (and presumes that everything else is done - valves perfectly set, timing spot-on, cable freeplay, etc.) - this method allows you to leave the airtubes in place and is electronic ignition friendly:

(with the engine NOT running,) Pull the rubber boot off the adjuster on the top of the carb - just slide it up the cable a little bit. Back the idle SPEED screws way out. Grab the cable on each carb and pull it up slightly (just a few mm) - repeatedly 'drop' the cable as you turn IN the idle SPEED adjuster. If the screw was far enough out, you will initially hear a dead THUD - until the screw is in far enough for the slide to hit it - at which point the dead thud will become more of a solid clunk (this sounds strange, but will be obvious when you do it). The exact transition point (thud to clunk) is where the idle SPEED screw is just touching the bottom of the slide - this is your ZERO point. Once you get each carb to ZERO, turn the idle SPEED adjuster IN one full turn. from now on, any adjustments you make to the speed screws must be equal - if you turn one half a turn in, turn the other half a turn, also...

Start the engine (ride around to fully warm it up if it is not already) and adjust the idle SPEED screws (equally) until the idle is around 1300 rpm. Now, adjust your idle MIXTURE screws for best running (this concept is the same as any carb - just remember that you are adjusting fuel delivery, not air). After you are happy with the mixture setting, turn the idle SPEED screws OUT (evenly from side-to-side) until the idle is where you want it to be (850-950 rpm). Shut off the engine.

Now, grab the throttle and turn it lightly until the freeplay is taken up (i.e., you don't want to move the slides, just take up the existing freeplay). Hold the throttle there and give each throttle cable a gentle tug to see if either one has any freeplay left. If so, adjust one or the other to equalize them. keep doing that until you get it to the point where the freeplay is equal - which means that the slides will begin to move at exactly the same time. You're done. It took me way longer to type this than it will take you to do it.

The "problem" with this method is that it does not do much to compensate for a weak cylinder - rather, it is a quick method to set everything equal between the two sides. If the rest of the bike is healthy, it's a pretty good method. With some experience, you can fine tune it form there without messing things up too much.

Here's a trick to help with the fine tuning (for Bings or Dellortos): Put the bike on the centerstand on a solid level surface. Start the engine and let it idle. Look at the way the bike is wobbling from side to side. Turn one of the idle speed screws and watch the wobbling. The farther away from balanced you go, the more it wobbles. Stand behind the bike and listen while you are playing around with this (or, better yet, while someone else slowly changes the setting) - you will be able to hear the changes. If you carefully listen as you do all of the above, you will be able to get it even closer.

I cannot stress enough that carb settings must be the last part of your tuning procedure. Don't bother setting your carbs without KNOWING that your valves are set - and, definitely check/set your timing PRIOR to carb tuning as opposed to after.