I can dang near take a complete bike apart with the tool kit that is sent with the bike.
There is one special screw on each carb diaphram cover that is a tamper proof torx bit. The rest are normal #2 phillips. There are also a lot of #3 phillips on the carbs and on the bike in general. If in doubt check to see if the #3 fits first before you try the #2. There are some "special" made phillips screwdrivers out there that fit these screws even better but i've always had fine luck with the craftsman.
The absolute most handy tool I have is a manual impact screwdriver (craftsman). This is the type that you hit on the end with a hammer.
The second most usefull tools I have are apex bit sockets (allen drive and #2/#3 phillips bit sockets).
A good dead blow hammer.
8, 10, 12, 14, 15, 17, 18, 19 mm sockets 3/8th drive (6 point deep is what I mostly use).
Don't remember the big socket sizes. Same sizes in wrenches.
Various length and thickness flat screwdrivers and even a couple you can sand down the width to make the perfect screwdriver for various places (A/F mix screw and main jet for example).
Torque Wrench as noted (craftsman makes inch and ft lb versions).
Mighty Vac (or craftsman equivalent)
Duck Bill Pliers (works well on the spring ring hose clamps). Standard selection of pliers and vice grips (not needed often but when you need them you need them).
Spanner Wrench (for adjusting the steering head bearings)
"coin" socket if you have to remove the timing inspection plug (not needed for most)
Various extensions
Various Allen wrenches (see noted allen sockets). I like my set from craftsman with the ball ends on the long end. Lets you get at and angle if needed.
Carb Sync Tool. Get one that checks all 4 at one time. My sync tool is a lot more expensive unit then most need.
Gasket Scraper (must use carefully since it can dig into the aluminum).
Flashlights, Flexible Magnet retrieval tool. Regular Ball Pean (and heavy one works sometimes). Gear/Balancer Puller (used only to remove the flywheel when the starter clutch goes bad).
Virtually all the tools I need to use (except the specialty ones listed) will fit into a 3 drawer hand carry box (and is literally what I have them in most of the time).
An ATV type lift is nice but not always needed. A car floor jack will even work well if you know where to lift the bike (depends on which end you want off the ground).
Sean