Well I am finally done round 1.  The Montesa is back together and running.  I tore it down to the frame, painted and rebuilt it.  New rear shocks, tires, seat and 1 new lower fork.  It took me 1.5 weeks to get the forks off and now I can rebuild the front end in 30 minutes. Fun and a lot of learning. 

I still need HELP!  Front forks are rebuilt but I have parts missing.  1 fork was seized - it was missing the lower fork piston bushing.  I had to get one machined and then honed down to fit.  It works amazing now BUT this fork is 1.5" shorter than the other.  The shock I did not rebuild it missing something in the top half  of the fork that stops the piston.  

Explanation - Front Fork - Top Nut - main spring, piston - So top half of fork when I look down I see a square stopper that stops the fork piston.  On the shock i rebuilt when you look in you see a stopper or spacer in the tube.  I did not want to try to push this part all the way up the fork tube in case it got stuck.

So I assume I rode it this way in the 90s.  BUT the forks are not balanced, so when you rebound only one fork would top out and the springs are not equal pressure.  Will it damage the fork over time? I found the manual but the parts are not listed anywhere. 
Thanks

Francis 

Both forks need to be working the same inside to avoid problems and for it to be nice to ride. It's not clear from your explanation what is going on. Maybe post photos of the fork internals showing right side vs left side