15% above tax, freight, etc. Sounds low, but we are not retailers. Take total cost and multiply by 1.15.

If it's a specialty item that requires a special trip, or a particular amount of research to locate, you may consider adding your time to the cost of the estimate/bill at your labor rate. Time is money.

This is just how I do it, and I've not had any complaints as of yet. If I have a particularly cost-concerned customer, I will explain the costs related to acquisition, storage, transport, etc. They, in a rare instance, may opt to acquire all or some of the materials themselves. Then I would supply a list with DETAILED spec info, and let them know that any improper parts that they provide cannot not be accepted. This invariably leads to them abandoning the notion and just letting me get what I need.