For the engine, it's pretty much what Mick71b said: spark, fuel, air, and compression are the things needed to make an engine run.
Spark: I'm not familiar with the electrical systems on these bikes, so someone else will hopefully be able to give you a good rundown on that. All I can really say is check every part one by one: battery have good voltage, coil operating properly, spark plugs have spark, etc.
Fuel: Start by checking the tank for rust, if it's rusty, clean it. Then the petcocks, do they let fuel pass, stop fuel, and not leak? Are your fuel lines in good shape, are they cracked, plugged, or worn? Find out what kind of carbs you're working with, rebuild them if they need it, or possibly right away so you don't get it all together only to find out they're dirty/plugged/non-operational.
Air: Pretty simple, if there's nothing blocking the airbox or the air intake on the carbs, you should be getting air. Running without filters will cause it to run quite lean with stock carb settings, so just watch out for that.
Compression: Easiest way to test it to rent a compression tester from Advance Auto, Autozone, etc. It should come with directions or you should be able to ask the person at the counter. If I remember correctly, most of the time the actual compression of a cylinder is not as important as the relationship the cylinders have to each other. That's not to say compression is not important, if you're very low it won't run for crap, but it's also important that the cylinders have compression close to one another. So if cylinder #1 has compression of 150 PSI and cylinder #2 has compression of 140 PSI, you're still ok(from what I remember on cars anyway). If they're far off though, that's a problem, and very low PSI is also a problem.
Hopefully that will give you a decent start on the engine, other than that my advice would be: run it one system at a time. Engine, transmission, brakes, suspension, etc
Fuel, air, spark.
