If I am unable to turn down those customers, and for whatever reasons, need to do the job for them - I tend to do a hefty mark up for my time and aggravation. They may not be sitting next to me while I'm working on their vinyl, you can be sure that I'm still aggravated while I'm working on the layout, clean-up, cutting, weeding, taping, delivery, and possible installation.
The most important part is to, at the very minimum, know your hard cost on material - what does the vinyl cost you for the different grades? is it reflective? is it frosted? is it camo? is it glittery? etc. Don't forget the cost of the application tape! Know what it cost you by square foot or square inch, whichever works best for you - then go from there. I don't use expensive squeegees or weeding tools, so I just consider that as part of the business expense since I get really great mileage out of it.