First the 'good news:" you have an iconic muscle-bike, stock, it defeated all-comers. Nothing-else compares. The Ducati Diavel comes-close, but sells fewer, and is more-expensive. And, you have to deal with the desmodromic vlave actuation, and tuning. Compared to that, cleaning your carbs occasionally is a cake-walk.
Now, the 'bad'-your rough idle is probably due to yes, dirty carbs, which is probably due to a rusted gas tank. Both are fixable by a skilled owner, but they are gonna cost you some sweat-equity. This is all supposition, and is based upon decades of ownership and service.
I suspect your gas tank is crusty. Take a flashlight and see what inside the filler neck tells-you. Do you see shiny metal in the bottom of the tank? Or do you see some dull, dark coating, or worse, a rusty, nasty interior, with gummy deposits? The latter is gonna require removal of the gas tank, and any of several methods of cleaning.
Some people like to seal the tank after cleaning it. If it appears rusted after cleaning, that's probably gonna be your path. You can try sealing the gas tank, Captain Kyle likes the KBS sealer product (do a site advanced search) but you have-to explicitly-follow the instructions, no shortcuts!
Cleaning can be done a number of ways. Vinegar (6% concentration or higher), Evaporust (expensive, but it works, vinegar does the same thing and is cheaper, time of soaking depends upon % concentration of the vinegar) or electrolysis (another search topic). Choose the one you feel most-comfortable to rely-upon. If you do the vinegar, remove the low fuel sending unit, and use a piece of metal and sealant to close-off that port. Leaving it soaking-in vinegar for too-long will destroy the potmetal of the low fuel sending unit.
A rough idle can be due to dirty pilot jets, incorrect carburetor synchronization, poorly-adjusted push/pull throttle cables, a dirt air cleaner element, a dirty fuel filter, etc.
Whatever is the issue, it has to be corrected to allow you trouble-free use of the bike. Once things are fully-sorted, you will laugh with great glee whenever you hit VBoost. It's that kind-of fun. Few stock bikes present this level of acceleration with such ease.
About your brakes, I'd check you have no glaze on the pads and sufficient pad material; smooth rotors, not rough, uneven ones, and that your master cylinder is full, the fluid is not opaque (if it is, you need-to change it! Look in advanced search for 'reverse-bleed' of your brakes) . You should not be-able to pull the front brake lever anywhere-near the handlebar, before you're able to lock the brakes.
You have the early brakes (1985-1989) which work OK if you have HH composition pads, but (this is my opinion) you have much to gain from, by at a minimum, replacing your pads with HH composition pads. I wouldn't bother spending my $ on anything else for those brakes and front end.
An easy upgrade, all bolt-on, is to add a 1993-2007 front end: triple trees, downtubes, sliders, and calipers and rotors. You get 43mm instead of the thinner 1985-'89 front end downtubes/sliders/triple trees/calipers (which are single-opposed piston), so your front end is larger diameter downtubes, sliders, two-pairs opposed pistons calipers, larger rotors, and it retains the stock early model wheel and speedometer sender. Throw some stainless steel hoses on that, with a set of HH pads, and you're going to have significantly-better braking. If you upgrade to the 1993-2007 front end, you can also upgrade to the early Yamaha R1 sportbike calipers which have the same bolt pattern/spacing as the VMax, but you may need to change out the hoses because of the mounting. Be aware that the later model R1's have radial brake caliper mounting, which does-not fit the Generation 1 VMax front end.
The 43mm front end downtubes and sliders are better (larger diameter) than the 1985-'89 set-up, and the two pairs of opposed pistons late-model brakes' calipers are better than the early brakes (which use a single pair of opposed pistons in each caliper) especially in HH pads and with the larger rotors the late model brakes use.