assuming the choke is working, the mixture screws could be turned all the way in and the bike should still start.
i think you may have been on the right track about this being either a fuel delivery or an ignition issue.
are the carbs getting gas? one quick way to tell is to open the drain screw on the float bowls and see if anything comes out (hold a cup underneath the bowl to catch any gas).....at the very least, that would indicate that fuel is flowing from the tank and through the petcock.
if your fuel petcock has a 'pri' position, try switching it to that instead.....in case the vacuum operated part of the petcock isn't working properly.
how did you make sure the spark plugs were working? keep in mind, a weak ignition system could cause the plugs to appear to work with the spark plug outside of the engine, but not spark properly when the spark plug is in the combustion chamber...
okay....so before he worked on the bike, it wouldn't run well at low rpm's? but after he got through with it, it doesn't run at all now?
i think you should try pulling the valve cover off, and then make sure cam timing is correct (when the crankshaft is turned to the timing mark, the arrows on the camshaft sprockets need to be pointing a certain way, also, double check the number of cam chain link pins between the two camshafts.....instructions are in the service manual), and check the valve clearances.
did you check the timing of the cams? if they were installed wrong, that would cause problems with measuring valve clearances.
once you've verified that the cams are installed correctly, then measure the clearances.....if you can't even get the feeler gauge in to measure the valve clearance, then that's a big problem right there.....essentially, that valve wouldn't close completely, and thus the combustion chamber would lose compression.
it'll be a little tricky since you have no clearance at all, so you'll need to go through a bit of trial and error before you end up with the correct shim....
how many valves have incorrect clearance? remove the shims from the valves that have the wrong clearance....keep track of which shims go where.
then go from one 'incorrect' valve to the next, and try thinner shims than the one that was on that valve originally, until you can actually fit the feeler gauge in it.....then calculate the correct shim size for that valve, and make note of it. then move on to the next 'incorrect' valve.
once you've finished going through all the valves, you'll have a list of the correct shims you need. compare this list to the list of incorrect shims you had removed.....you might have some which match, in which case you can just use those in the appropriate valves. the ones that you need but don't have, you'd need to buy.
just take your time, go slow, and you'll be okay......double check all of the valve clearances when you've replaced the shims.
when you say 'Turns pilot screw fit in 1/4 turn', what exactly do you mean? that you can only turn them in 1/4 turn (meaning the screws are only 1/4 turn out), or that you turned them in 1/4 turn? if the screws are only 1/4 turn out from all the way in, that's a bit too lean.
you don't need a timing lamp for anything, the ignition timing is electronically controlled.
try turning the pilot screws all the way in until they stop, and then turn them all the way out 2 turns. this way, you know exactly where you're at in terms of pilot mixture......if you just turn them in without knowing where they were to begin with, it won't really help much....
is the bike running rich, though? did the plugs come out very dark?
i don't know the exact float height for your bike, although a fairly good rule of thumb is to set them so that the 'lip' on the floats is parallel with the float bowl mating surface as the tangs on the floats just touch the float valves. (your mileage may vary, though)