if you think the pilot jets are small tolerances wait till you start messing with the needles. I little bit of crud naked to the eye can make your bike run too rich. Moving the needles two tiny notches can make your bike go from too rich to too lean. Just like that. Then after all that you need to vac sync all over again.
I wouldn't worry about how far the slides go down just adjust them with a 1/8" drill bit on the engine side of the carb. If everything else is clean: all jets and valves and air passages and needle surfaces, floats are adjusted (just as the float tab hits the plunger with no pressure) and work properly, put the carbs back on the bike. Double check the floats with the clear tube tool. EVen without the airbox attached it should still start and run good enough to give it a vac sync and you should be riding it soon enough. I usually don't put my ancillary stuff back on, like hoses and intake plenum rubbers, until I know I'm done with the carbs.
