Edward, let me take a crack at this and hopefully others will chime in.
First, I have some questions:
Is the timing set correctly?
Have the carbs been cleaned (all the passages and jets clear)?
Has the bike been running, just not that well?
Any other info about the state it's currently in would be helpful.
Now your questions:
How can I tell if the fuel is leaving and getting into the chambers?
Generally if fuel is making it into the combustion chambers and you can't get the bike to run, after several kicks the plugs will start to foul (get wet). If you remove the plugs you should smell the presence of gas in the combustion chambers.
Do I need all of the covers on and air filter in place?
No
Should I be able to visually see a "spritz" get sucked into the engine?
Probably not
What parts of the carbureator should I check for proper adjustment and flow?
The air screw to the left of the venturi needs to be set correctly. About a turn and a half out from seated.
The slide position should be set with the screw at the top of the carb cap and the throttle cable adjusted with the screw next to that.
The choke cable needs adjusting.
The float needed to be set prior to assembly.
and the slide needle clip needs to be in the center position (to start).
I don't think I missed anything...and you've probably been down most of this list.
What does it mean to "flood" the engine and how can I check it?
An engine is referred to as flooded when too much fuel has gotten into the combustion chambers (and in the case of cars, the intake manifold) causing the mixture to be too rich to fire. At that point the engine (an importantly, the plugs) needs to be allowed to dry out (fuel evaporated). In some cases this will foul the plugs either requiring cleaning the plugs or replacing them.
Hope this helps and as I said, hoping others will jump in as well...
...bert
