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Have been working on getting my 79 kz650SR up and running. Bought it not running. Currently running….like crap. Cylinder 4 is cold. When I pull plug wire while running, no change. There IS spark getting to the plug. DI’ve already tried different wires, plugs, swapped the coils to see if one of the coils was bad. Same problem. Points are new and set properly. I have not done an actual compression test but there is definitely pressure there. Could I have done some incorrectly/missed something when rebuilding the carbs? Could this be an issue with the factory vacuum system? Is there a best way to test if fuel is getting to the cylinder? When I pull the plug is dry. I would think if it’s not firing, there should be excess fuel left over. I’m close to pulling the carbs again but dealing with those carb boots is a pain. Any help would be great. 

Have you insured the proper fuel level in each carburetor by using the clear tube method?
Have you checked the valve clearances? One could be bent or stuck.
A compression check would be helpful, though they are only accurate when the engine is warm. A leak down test would give you a better idea of where the problem is, if there is a problem with cylinder pressure. You may be able to borrow or rent the tools for that from a local auto parts store, though you will need an air compressor to do it.
You mention the vacuum system. I believe that the only vacuum tube on the 650 SR goes to the fuel valve, or petcock, on the fuel tank. I think it connects to a vertical tube on carb number two. There is a vacuum port  on each carb holder that should be plugged with a tight fitting rubber cap. Carbs two and four have what looks like vacuum ports ( small brass tubes) coming out at about a 45 degree angle. They are bowl vents and should have a hose on each that is open to atmosphere. For now, it is ok to start it without the vent hoses.

When I put my KZ1000 back on the road, I had the same problem. Plug fired, but looked brand new while the others had some wear, after 4 or 5 hundred miles. It turned out the float bowl was stuck and fuel wasn't getting through. My KZ has drain screws. I opened mine and no gas came out. I removed the bowl while the carbs were still in place and freed it up. That fixed mine.

Thanks guys, I will check if fuel is getting to the carb then do clear tube test and go from there. Thanks for the ideas. 

You could spray starting fluid into #4 while it’s running to see if the cylinder fires.

Sometimes tapping on the float bowl while it's running may dislodge a stuck float.