There are two TDC in a 4 stroke engine for every cylinder. One, is the compression stroke, where BOTH valves are closed, and at TDC you will have clearance to set your valves. The other TDC is on the Exhaust stroke, where the intake is closed, and the exhaust valve is open. You will have no clearance there for the EXHAUST valve. This is common for each cylinder. Now, Scott is telling you truthfully, you are missing rudimentary knowledge as how a 4 stroke engine works. Because of this, you have confused yourself into a corner, and have multiple issues going on, which may all be due to this one thing.
If you have had the valve cover off, and haven't installed it back correctly, that could be a cause of the rocker arm binding, and no valve clearance. Hopefully nothing was damaged when you did this, then cranked over the engine. For valves to be successfully adjusted, the valve train must be correctly installed. Part of your valve train is in the rocker cover, or valve cover as it is know also. I would remove it again, and back off all the valve adjusters, then using the RUBBER BANDS, hold the rockers up as you have been instructed to, and re-install the cover. Prior to doing so, I would turn over the engine, observing the intake and exhaust valves to determine when #1 TDC occurs on the COMPRESSION Stroke. As you turn over the engine, one valve will open on #1 cylinder, then the other. At the #1 TDC (there are two) that BOTH valves remain closed (both at same position, closed) leave the engine there, and make sure your timing marks in the points plate point to 1-4. THEN re-install your valve cover, using the rubber bands to hold up the rockers on all 4 cylinders. Now, without moving the engine, set the valves on #1 cylinder, and follow the instructions that Scott provided to adjust the rest of the 3 cylinder's valves. You MUST start at a know position, in order to achieve success in this. If this description is confusing, is there a friend close that has knowledge on motorcycle mechanics, that could assist you?
Charlie