It's both simple and complex, because of the relationship between carbs and engine. There are a few good manuals out there to set up weber carbs. I'd recommend buying one, but you can probably find a setup guide on the net if you start with google.
If you've never had the carbs apart, then you might want to inspect inside and see if they look clean. Make sure all the jets are right before you start adjusting.
IF the engine is all in good condition, and the carb mounts, then balancing the air flow through the carbs at idle is a good place to start (either with a flow meter or the old school way with a tube in your ear trying to get all the noise the same). A colour tune kit can be useful to get the idle mixture the same on each carb as a good starting point as well.
I normally start by setting all the idle mixture screws to the same number of turns from the stop, and then check it.
However, the big disclaimer on carb setting, is the carb balance depends on the balance of the engine. If you've got an imbalance across cylinders (due to tappet clearance, compression problems, or anything else) then the carbs don't want the same amount of air/fuel to meet the individual cylinders' needs. A compression check on the cylinders isn't a bad place to understand what you're dealing with. Also, any sort of leak at the carb mounts will make the whole exercise futile. Re-reading your post, it sounds like you've already covered some of that off.