Jim,

Although you sell services, it sounds like you actually handle them just as anyone handles products and using OE with its alternate price lists could work well for you. Do you need detailed descriptions of services provided, or is a basic item description sufficient?

"The quote will list line items for the entire project and the samples will trickle in over a period of time."
So the quote becomes your order, for which you will create more than one invoice, invoicing for each part of the project as it is completed.