I have only cleaned (with some steel wool) the frame - some tarnish/dirt had formed over the years on the chrome surface. Have not lubed the joints, although this might be a good idea. One thing to make sure of is that all of the bolts are in tight. They sometimes work themselves loose.
As for the fit, I have to do the same as you: after I press down the rear latch, I have to tug pretty hard at the front to get it lined up with the holes. You could try moving the frame + top forward by loosening the bolts that hold the frame down, while also moving the rear latch. Others may be more experienced in this department!
Final tip: I noticed that between the canvas and the folding part of the metal frame that meets the top of the side windows (I hope you are still with me) there was a gap that I could see straight through (about a half inch in the middle, where the gap was the widest). I noticed the same on other Pagodas. What I did to remedy this (lots of wind noise at speed) is I cut strips of self-adhesive black insulation foam, about 3/4 inch thick) that I glued onto the top of the metal frame; now when the top is up, the foam seals the gaps and no more wind noise! (which makes for more comfortable driving longer distances). I will try to remember to take some photos next time I'm at the garage.
Cees Klumper in Amsterdam
'69 white 280 SL automatic