First, if you have glue-in glass on your 69, consider swapping to 70 glass.  It will avoid issues later on with the regulator separating from the glass.

There are two tracks on the 69 glass and both must be adjusted parallel for the window to be able to raise and lower easily.  Just like Rudi suggested, the old grease can dry out and make things hard to operate.  The rods are adjusted with some screws that come up through the bottom of the doors.

If they are really difficult, remove and clean all the parts and apply new grease if you want them to work right.  And as Rudi mentioned, check the rollers.  They are really inexpensive to replace and just snap onto the shafts.

Power windows is a good idea to replace the antiquated Mustang regulators but, on your 69, you still have to get the vertical guides working smoothly.  There are some C- shaped guides that mount to the window glass, and they have plastic inserts that slide on the tubular guides.  Be sure the inserts are not worn out and they are not binding on the guides.  I have even had the guides break, usually right where the vertical tube is attached to the adjustment flange at the bottom.  They can be rewelded if that is the case.

It might be as simple as removing the door panel and lubricating all the moving parts, or you may need to remove everything, clean and relube and reinstall.