I rebuilt the carb's first mostly because I thought they needed the most attention. They were i nsad shape, the bowls were leaking, previous owner had them siliconed on, took forever to get them cleaned up.
Of course. The carbs have to work before you can tune them. But, the carbs aren't tweaked during a normal tune up. They are pretty stable, adjustmentwise once they are dialed in. But, tappets wear, points wear, and timing changes occur during normal operation. Restoring these at tune up time usually means your can ignore the carb adjustments. But, if you tune your carbs with these other things out of whack, they won't be right when they are set properly and you will likely have to re tune the carbs. It's your time. Do what you want.
Did you replace the orings that seal the main jets to the carb bodies? Leakage there can make things problematic.
I'm not certain how to check the timing. I'm assuming since it fires right up that it's in time.
Bad assumption, I think. It's harder to solve an equation with unknown variables. And, until you know... Anyway, you can download the shop manual from elsewhere on this site. All the tune up proceedures are explained in there.
I'm going to go check the valves, and put some new gas in it today. The tank was pretty clean, and I have new filters on it. I dont have an airfilter in, would that make a difference?
The slow jet orifices are .016 inches in diameter. Does "pretty clean" means the bits you saw were smaller than that?
Air filters do make a difference, sometimes huge. And, unless you are going to run the engine like that 'til it dies, it's pointless to tune carbs until one is installed.
Some background.
Fuel flows through an orifice when there is a pressure differential one side to the other. The more pressure differential, the more flow. In your carbs, one side of the orifice is always at atmospheric pressure. The other side is subject to the suction from the running engine and the venturi effect in the carb throat. Operation of the choke increases the suction effect, drawing more fuel through the jet orifices. An air filter presents partial restriction (like partial choke) and therefore effects fuel air mixture ratios. Carbs should be tuned to compensate for this restriction.
FYI, air filters keep dust particals from being blasted onto the cylinder walls, eroding them.
Good luck!