Before I retired, I turned out over 100 client restorations, custom builds, major overhauls, and total refurbs (wake-up/make-run).
In every case, I always charged a flat percentage on the parts and subbed-out work (machine shop, chrome platers, painter, etc), a nominal charge for consumables & materials, and carefully estimated my labor based on experience, then added a 10% cushion for the more involved projects. My rate was $25/HR and I was just able to keep a family of 3, then 4, fed & clothed with 1 or 2 trips to the beach every summer.
The GREAT thing was getting to travel all over to collect and deliver client bikes, and to take advantage of volume buying and tradesmen to also restore a dozen of my own bikes over the 15 years that I was in the biz.
Win-Win.
EDIT-- I forgot to mention the 6 or 8 MAJOR lot purchases and "twofer / threefer" bike deals I acquired over those years. Those were totally icing on the cake, and in fact I still have several hundred pounds of parts that bought as long ago as 2004.