The only way to bill it out is BY THE HOUR! Spend some time putting everything out on paper, then double the time you think it will take. Double that again.
\Talk to your potential customer, lay out the build plan, what you will do and the estimated times. Broken, rusty, greasy, mismatched parts are HIS problem not yours- don't let that change. This is a lot of work and plenty of room for failure. One thing I will throw out, call a few quality shops in your area and ask what their posted rate is, you can add 50% for custom work. The last shop I worked in was $85/hour and that was 10 years ago. Also, NO WARRANTY on customer supplied parts. That markup is to CYA when something breaks.