Jay,
1st thing I would like to say is, that's great that you want to only have legitimate Contractors that do reputable work, doing the work. Keep in mind that Your costs will be more compared to the guy you find hanging around the big box store because of their experience and reputation. Then I want to add, the questions you asked above are exactly why I do not work with other real estate investors, they are actually insulting. If you are looking for a reputably Contractor, those are the ones that will give you a price for the project, be there to complete the project and complete it on budget. you asking those questions sounds like you want to micro manage their company, does anyone micro manage your co.? If you worry about price gauging on materials, then open your own accounts and purchase the materials yourself, this way you will not have any reason to question the price. Just to let you know, that will probably eliminate most of your top contractors, Contractors usually have more than one project at a time going and time is of the essence for scheduling, relying on someone else to get the material there can delay a job a lot. Where a contractor buys their material is of no importance to you, if they give you a fixed price for the project, as long as they get the material there, get the project done and for the price they gave you, this is their business and if they make a profit on the material then they are happy and have no problem getting the job done for you. I am not saying that all Investors here are the same, but too many like to buy the materials themselves and try to micro manage the contractors companies, I am sure that a good number of the stories here on BP about bad contractors have 2 sides to the story that people do not get to hear, I personally have just made it my policy not to work that way and have been working by word of mouth for 32 years as a general Contractor.
Now if you are talking about Time and Material project, then I would recommend you open an account at a local lumber yard, have the contractor purchase the material on your account, this way you know what exactly has been spent for everything. Also let them order and schedule what they need and when they need it.
Keep in mind, the contractor is running a business, he will charge you a percentage on top of material and labor, if you get it or them, they need to cover their overhead and make a profit.
If you are looking for A good contractor, the best place to start is your local Lumber yard - not the box stores. the guys at the lumber yard will know the most reputable contractors in town because they will know them personally, deal with them a lot and also know of feedback from the contractors customers. always ask any contractors you are thinking of hiring for a list of clients as references, and call them, they will know best about how a contractor is and give you unbiased answers to any questions you have about a contractor.