Once you get it started, feel the exhaust pipes. Both pipes should immediately warm up; if one isn't, then you know that cylinder is missing.
Does the bike have adjustable valves? If so, better check your valve clearances; you might have a valve that's not closing, which is very bad and can cause bigger problems if it's not corrected.
If you are able to narrow it down to a single cylinder, then you can probably figure out the problem from there. If the cylinder will hit if you give its carb SMALL shot of ether, then it's not getting fuel
Fresh plugs never hurt anything, either.