If you rebuilt the entire engine, I assume you used feeler gauges to check the cam to valve shim clearance, and replaced shims appropriately with (usually thicker) shims to get the proper clearances back? I think the factory spec, cold engine-not been ran for at least 12 hours) is around .02-.08mm acceptable clearance. Been since fall that I last checked mine, I can't remember the spec exactly. Shims are about $7 each, sometimes you can use discarded shims on other valves needing that size swapped in.
A little re-hash, but think of it is reinforcing the tried and true suggestions of all the ace mechanics here - Clean clean clean carbs, good sharp pointy tips on fuel screws (nothing broken off in carb bodies I hope!), new carb o-rings, new intake boot to head o-rings, GOOD CONDITION intake boots, carbs at suggested baseline settings with 120-ish mains, needles 1 clip below the middle (lowering the clip position actually raises the needle), carbs visually bench synched precisely (easy to do), get it running and set idle speed, put a good differential manometer synch gauge setup on it (not the dial type vacuum gauges), run the bike with a window fan in front of it to cool the engine, tank strapped sideways across the seat for access to the carbs (may need extended fuel hose), carb tops off, 8mm wrench I think and a good fitting flathead screwdriver, synch adapters installed, and fire it up! very little movement on the slotted flathead slide shaft will make a good difference on the gauge, and tightening down the locknut will also slightly affect the synch, so try to predict a slight difference after tightening the locknut down.
As for adjusting the pilots, I am still trying to get mine fine-tuned, but others will tell you to start with the fuel screws at about 1 turn out, very free flowing straight through exhaust may need 1-1/8, but keep in mind 1/16th turn makes a big difference on the fuel screws. Then play with the air screws to get the highest rpm. If you have any misfiring, I have found a timing light pointed at anything will help you find the range in between lean misfires and rich(fouled) misfires where you don't have any misfires.
Then.... ride it, and see how it feels power-wise when you transition from less than 1/8 throttle (pilot circuit only) to the needle jet and jet needle. If you are lacking something in a smooth continuous-power transition, you need to try tuning the fuel screws in or out and re-tune the air screws. Cruising around the neighborhood for 20 minutes at never more than 1/8 throttle, and then pulling the plugs to check the color should help you determine whether the source of your not-smooth-transition means your fuel screws are too rich or too lean.
Get the pilot tuned, then go on to WOT (wide open throttle) plug chops. To do this properly, you really really need to find a SAFE desolate road or highway entrance with no law enforcement presence, driveways, intersections, turns, etc, preferably uphill, on a set of plugs that have been in the bike for at least 30-40 miles, and start from a stop and run the bike like a drag racer at wide open throttle for at least 7 seconds, if not 10 if that is possible. It is of my opinion that you need to keep it above 4000 rpm to get the mains sized properly, if not 5000. Then the critical part - hit the kill switch, pull in the clutch, and close the throttle 100% all simultaneously. pull over, remove all 4 plugs, put them in a safe place (they are hotttt) where they won't melt anything or get all scuffed up, and take them home. install a spare set of plugs, of course.
Now, some say you can use a magnifying glass and a flashlight to inspect the color of the plugs' carbon coloring way down inside the threaded area at the base of the insulator, but most people prefer to "chop" the plugs' threads off with a cutoff wheel, hacksaw, sawsall, or bandsaw. This exposes the insulator all the way to the base. If you have a surplus of unburnt fuel, the furthest area for the flame to reach is deep down in that crevice of the spark plug, so the fuel will not be completely burnt, and you will see a dark brown or black sooty ring at the base of the exposed white porcelain insulator. Too rich on the mains. If it is too lean (makes lotsa power but runs waaaayyyy too hot), all the fuel deep down in there will be completely combusted and the heat will burn off any soot deposits that are there. You need to get it to the point of having a light brown or tan ring at the bottom. I'll see if I can dig up a handy photo. Swapping main jets in and out will be the route here. jetsrus.com sells cheap mikuni "OEM equivalent" jets if you are unsure if your sizing is in the ballpark. after you do a chop on the 120's and you need different mains, order a couple of sets in the sizes up or down that you think you will need. 122.5 or 125 would be the absolute largest I could imagine, and you might end up with as low as 110-115. Depends on the engine condition, valve condition, ring and cylinder wall condition(are they broken in yet? ride it a few hundred miles after getting a moderate state of tune and re-test), air filter cleanliness and proper amount of filter oil if K&N or UNI.
Now you can do some plug chops for about 1/2 or 5/8 throttle position to check the needle height, but you really need to have the proper mains in before you can fine tune the needle height. it helps to wrap a piece of masking tape on the right controls next to the grip, and mark a reference line on the grip, and similar line on the tape on the controls next to the grip. Then twist it to full throttle, and mark the controls tape with a line corresponding to the grip reference line, and that is WOT. Now you can put a mark at 1/2 throttle and 1/8th throttle to help you when doing plug chops and pilot adjustments.
There is also a Gunson Colortune that helps you get perfect combustion mixture on the pilots by monitoring the flame color. dark blue is perfect, light bliue or blue-white is lean, yellow flickers or solid yellow flame color is too rich. These work great on VM carbs, but not CV type vacuum slide carbs.
And another note, CV carbs were introduced to eliminate user error that makes VM carbs act up momentarily. If you instantly whack open the throttle pretty far on a VM, you immediately let so much air into the carb that you lose most of the vacuum momentarily, which kills the air velocity through the carb for an instant because the carb venturi effect relies on high velocity air siphoning fuel against gravity up into the carb. If you rip open the throttle on a Constant Velocity style carb (vacuum operated slide, not mechanical-tied-to-throttle-cable), compared to the same on a VM manual slide carb, you will think the VM isn't very good at this move, but if you open the VM throttle a little more gradually, you will reach a sweet spot where you maintain enough velocity of air in the carb to keep the fuel flowing in copious volumes to produce great acceleration as you are increasing the airflow with precise throttle twisting. The CV carbs basically are designed to do all the thinking for you, so when you whack open the throttle instantly to WOT, the slide only raises as much as it needs to in order to maintain enough air velocity, and it will raise the slide at the same rate as you would find is the best throttle twisting rate on the VM carbs anyway.
CV's have a butterfly throttle blade in the outlet of the carb that blocks the flow even somewhat at WOT, therefore you will see a 79 model with 26mm manual slide carbs and the similar 1980 model with CV's will have a 32mm vacuum slide carb. similar airflows. The VM's (and Keihin CR's, etc) are considered the best for all out speed and power, but CV's give more control with less thinking/throttle precision and are favored by road racers. Flat out drag racing, the VM's will have a slight edge. Wow, that was a lot of info, I hope I didn't overwhelm you. I've learned all of this stuff from the help of all the awesome people on GSR and a few other sources occasionally, from the past 5 years or so. Thanks to all. Please correct me if there are any discrepancies or omissions.