if you've lined everything up, adjusted your pushrods properly, confident that timing is close, and your rear cylinder is cold and appears to not be firing, then i'd look at the coil

 

Spark plug to the rear cylinder is getting fire, but rear cylinder will not kick in.

 

Take your rocker covers off, bump it over and watch what the rockers are doing? Shot in the dark but seems you might see if rods are timing right?

 

if piston is dead in cylinder, and you're getting fire to the plug, then i'd pull rocker covers off and see what the pushrods are doing to rockers and valves

 

Whats the compression reading on each cylinder.

 

Compression was 200 psi on each cylinder, within 1 lb of each other, before I pulled it apart. I'll do another compression check tomorrow and see what I've got. The only reason I pulled it apart was because it had developed a loud tick, off and on. Thought a lifter might be going south on me. It was really loud at 68-70 mph. I can't imagine what I've done to screw things up this bad. I've installed lifters and adjusted pushrods before with absolutely no problems. This has me scratching my head.

 

just a long shot...but maybe one of the pushrods are stripped a bit, and it's not holding its tension anymore?

 

I think I've figured it out. The cam is twice the diameter of the pinion gear. The cam has 42 teeth, the pinion gear has 21. Takes two rotations of the pinion gear/crank shaft to rotate the cam one rotation. I think I have the stroke off by 180 degrees when I reinstalled the cam. I think the solution is to remove the cam, rotate the pinion gear/crank shaft one full revolution then reinstall the cam and align the dots. We'll see in a few minutes.

 

That's not going to change anything, the dot rotates with the crank so every time it is up the crank is in the same place. The same goes with the cam. Your problem is in the adjustment or cam is not in properly. You may have done it before, but this time you are doing something different. Do you have the right pushrods in the right places?? How many threads per inch are your pushrods ?? Make sure the lifters are on the base circle by watching them. Hope this helps.
John

 

You sure your looking at the correct mark on the pinion gear? it's normally a line, and not a dot.

Just to verify there's no damage from valve to valve, or valve to piston contact, loosen or remove all pushrods, take your compression gauge hose and remove the shrader valve in the end, screw the hose in plug hole and connect to your air compressor line.
Listen for major leaks at carb and exhaust, it'll be obvious if a valve is damaged.
No need to find TDC for the test, make sure bike is in neutral, so it doesn't roll when you hook the air line.