Of course you will be limited by the top as it's cut, stapled, and glued to the carriage, but you should try to get the top relatively square for a starting point.
After that the quarter window is relatively simple (if not satisfying for a perfectionist), with the three bolts at bottom plus the two up top giving you most of the adjustment (there is also a stop for the regulator that should be loosened). Get it to fit snugly up top, tighten the bolts, and then roll it down and see how it fits. With a proper top/carriage alignment, I think you will get a pretty good result, but with a third, fourth, or moreth iteration top the fit may be a matter of compromise. It took me about six attempts to get relatively happy with the fit between the top and the quarter window, and longer once the door window was part of the mix.
Other_shoe can you tell me if one can adjust the quarter window to line up with the door window? Mine is close at the bottom but a gap at the top. I cant see how to adjust this.