If the top isn't latching right then the top frame is out of adjustment. Or you badly bent it when forcing it. If your header bar ( The bar that locks to the windshield header ) had guide pins sticking down, they should be centered over the guide holes in the windshield header. If they are off center 1/2 " then you won't lock it down.
Do you know about shrinkage ? As the temperatures drop at night and you try to put the top up at night it can be very difficult to lock the top down, thats because the top material is more taut and can't stretch like it does when the sunny is beating down on it.
I'm not sure where this nut / bolt is that you lost. I seem to remember an adjusing set screw at the first hinge point between the first & second rail. I can't remeber exactly what it adjusted, it might of just been the angle of the front side rail.
Another point that may have lost the top alignment is where the rear of the frame work is bolted into the body behind the rear seat.
Top work is very hard to do and is best left to a professional. I'd say to have a shop check it out that works on tops.
The type of strain you have on your lock latches may be enough to break the latch hooks right off the handles. Then we'll see you driving down Main Street with a nine inch wide band of grey duct tape across the front edge of the top & windsheild.
good luck.
========= Harryface =========
1991 Pontiac Bonneville LE 3800 V6 ( C ), Black/Slate Grey _~_~_~279, 495 miles_~_~_
~_~_~_~_U.S.A._~_~_~_~_~_
~~~The Former Fleet ~~~
89 Cavalier Z 24 convertible
78 Holiday 88 coupe
68 LeSabre convertible
73 Impala sedan