Improper valve clearances wouldn't really have that much effect on how rich the bike is running. Just a few questions to help us to help you out:
Year/Model of bike and CC
Main and Pilot jet size
Turns out on the mixture screws
Jetted, stock?
Aftermarket pipe?
Float height on carbs?
Emulsion tubes worn in the carbs(could be it as it would dump alot of extra fuel on the slides)
Needle position or shims? (A really rich needle will also dump fuel unnecessarily)
If you don't know all the info just try and do the best you can. A big hint would be if the bike has been Jetted with an aftermarket pipe. Perhaps the previous owned did a really crappy job jetting it(we see this alot) and now it's super rich. Usually when there is alot of fuel dumping into the slides it can be these things:
1. Mainjet way too rich
2. Mainjets actually worked themselves loose and it's just a big ass hole with the emulsion tube the only thing holding the fuel back(saw this once but usually only one carb will be bad not all of them)
3. Needle extremly rich will also dump fuel
4. Float height set too low which will flood the carbs
5. Pilots way too rich or mixture screws turn out too many turns will make the low end rich
6. Pilots working themselves loose
7. Emulsion tube is ovaled and worn dumping extra fuel in there when the slide comes up(can be sort of temporarily fixed sort of by lowering the needle a notch or two)
8. Air filter dirty and clogged
9. Emulsion tubes loose or O-rings dead
The best advice I can give you is take one of the outside floatbowls off so you don't have to pull the entire carb bank off and take a look in there. Unscrew CAREFULLY the mainjet and pilot jets and write down the size. They should be marked with a number, mainjet sizes for a Bandit 1200 will be like 100, 110, etc in steps of 2.5. Pilot jet sizes would be around the 15, 17.5, etc. Dynojet mainjet sizes will be in steps of 2. Mikuni jets are in steps of 2.5.
If you have a Dynojet kit in there, they use crazy ass rich float height settings to achieve their jetting but their Mainjets are smaller. If you have a Bandit 1200 the Dynojet kits suck for some reason on this bike. Since the Dynojet mainjets are actually smaller than stock sometimes people after maxing out on the Dynojet kits will order Mikuni jets instead which really make it rich, it just turns the jetting into a cluster phuck. Anyway don't sweat it even if it's all messed up depending on the model we can suggest the proper jets to try and sort it all out.
For example I have a Generation 2 2005 Bandit 1200 with a Holeshot jet kit installed:
Mainjet: 112.5
Pilotjet: 15
Mixture screws 3.75 turns out from lightly seated
Float height: 13mm
1.5" extra hole in the top airbox lid
Stock filter
5 shims on the needle(or if you have an adjustable tell us how many notches from top)
Muzzy Slip on with mid-pipe
If you get this sort of info it would really be helpfull. For example one guy had some winner install a jetkit on a Stock exhaust and intake.(WTF?) Needless to say it was rich as hell, you can't just add fuel or air without adjusting either to keep an apropriate ratio. See what you can come up with and we can help you more. Just be REALLY CAREFULL with those jets, they are soft brass so don't go jihad screwing them in and out, nice and snug is fine.
If you have the pilots out only 3/4 of a turn you either are compensating for a super rich mainjet as you said the top end is crappy or the emulsion tube has ovaled and is dumping extra fuel in there. Or your float height is crazy low or your pilots have been changed out for super rich ones. Did you take a look at the emulsion tube to see if the brass is worn? The emulsion tube is the hex nut tube that the mainjet screws into. You want to check to see if the top of the emulsion tube where the needle seats is perfectly round and not ovaled. Here is a pic of an ovaled emulsion tube needle seat:
Is it all the carbs that are rich? Which would suggest the settings are off. Do you have a stock or a K&N filter? If it's a stock filter the bike would run alot better with a K&N if it really was that rich, however the real solution is to jet it to what your normal setup is.
From just your symptoms with zero information I would guess the mainjet is way too rich. Once you have the mainjet sizes, etc we'll be able to help you more. These bikes are almost stupidly easy to tune so if the previous owner phucked it up don't worry about it, we can probably get you set up quickly. Black smoke and running better when cold than hot is a sure sign of richness. Valves only affect the size of the fuel/air charge not the ratio of fuel to air as the wet slides will attest to is way too rich. Is your needle adjustable? If so lean it out one notch for fun by moving the C-clip UP one notch and see if you suddenly get some more power when warmed up.