76 KZ 900 gearbox outer cover won't mount even

Good evening gents,'
This bike is new to me, clutch cable wasn't functioning and was detached. I removed the gearbox cover to attach the clutch cable and clean out all the gunk around the chain area. As I was cleaning, the pushrod for the clutch pulled out about an inch. Now it doesn't seem to seat correctly into the old position. Since that happened the gearbox cover doesn't push in all the way even to the engine case. What did I do? Did I mess this up completely! Should the push rod pull out or is it broken? I don't want to pull it all the way out. Any assistance is greatly appreciated. Picture attached. thanks in advance.

I've been reading the manual and there isn't anything mentions the clutch pushrod. I got it flush to the engine case and hand tightened the bolts to hold it on but now the clutch lever doesn't pull in at all. very stiff. What is the problem, any ideas. I ve searched on the forum topics but seems like there are many different issues discussed. I haven't touched the clutch, just the clutch cable was the initial issues. Thanks for any help.
 

I found this, so I will pull the push rod to check for any junk and clean it. I bought this as a non running bike, clutch cable wasn't connected. I am beginning to wonder if the clutch isn't working. I can't start the bike yet so question, is there any way to check to see if the clutch is working ?

The clutch cable is harder to lube than any of the other cables. I would first change the cable. You MAY have one that is just gummy from rust and age. Next, there isn't much to a Kaw clutch. The clutch cable pulls on a plastic pivoting worm gear. This gear pivots inwards and pushes a long rod that goes across the engine to the clutch. The long rod has a ball bearing between it and the clutch pusher. First change the cable and pull out the rod that pushes and make sure it isn't bent or has been heavily greased in the past as the grease picks up crud and could make its action bind. If that doesn't do the trick, to take the clutch apart, you need to get a new clutch gasket. If the original phillips screws are still in place, make sure you use a hand impact driver to loosen them. Then remove the screws and scrape off the old gasket from the mating surfaces. There are six 6mm bolts. Remove these. The bolts hold the clutch springs. When the rod pushes the ball bearing that pushes the clutch pusher, the springs provide tension and return the plates closed... To get to the plates, just pull off the pressure plate which is also held on by the six bolts. The plates just pull out and alternate between fiber and steel plate. Behind these is the pusher and if you pull it out, the ball bearing can fall out so keep and eye out for it. The ball bearing can't come out on the cable side. As far as what to look for in an older Kaw for the first time are the correct number of plates, warping of plates and wear. A shop manual will give you the specifics and specs. If you don't have one, a link to the KZ900 Kaw Factory Service Manual has been posted in the past... somebody scanned it and uploaded it just recently.

Before tearing the clutch apart, make sure everything else is in order. The clutch lever pivot should be cleaned and greased. Get one of these  www.z1enterprises.com/yamaha-xs650-cable...ubrication-tool.html  and a can of cable lubricant. The clutch cable is not hard to lubricate. If there is obvious rust in the cable, or if there are broken strands, replace it.
While you have the cover off, be sure the release mechanism is clean and properly lubricated.
Yes, pull the rod out and be sure it is clean.
After putting it back together, adjust the cable using the procedure in the factory service manual.

If it still will not release, the plates may be stuck after sitting for a long time. There are ways to loosen them without taking the clutch apart.

Thanks Texas KZ, never knew of the cable lubricator. will check it out.