PCB inside a parallel port cable case
To answer your first question about clearance, I wouldn't worry about making the PCB slightly smaller than your enclosure. To begin with, the solder joints between the DB25 and PCB will hold it securely; I would also recommend adding pads on your PCB for all of the pins that you can (even unused ones) to increase mechanical strength, and increase your trace widths to prevent any mechanical stress breakage.

Regarding your second question, component availability is always a concern. You can reduce some worry by designing around the most widely available, high-profile manufacturer's connector case as you can find, or, as others suggested, by purchasing several of these cases from different reputable manufacturers, and redesigning your PCB to fit as many of them as is feasible. If you find you have too much wiggle room with certain cases, you can always pad the case with foam or rubber, or a dab of hot glue.