There isn't a simple answer to the questions you're asking. I'll do my best to give you a summary below, but first, I'll make a recommendation:
Take the numbers @Jeff Copeland and I gave you ($150-$200/SF) and do the calculations to figure out a rough estimate how much it will cost to build this house. I'd recommend using the higher end of that range since it sounds like you want to do some upgrades and you always want to leave yourself a healthy margin for error in construction. Don't forget to add in an additional costs for demolition, plans, and permitting. Do the numbers make sense? Will it be profitable? Is doing a tear-down/new-build cheaper than remodeling what's already there? If the answers are yes, then your next step is to find a local architect and explain your needs and budget to them. They will be able to draft plans for your house (for a fee, of course). Once the plans are complete, get bids from multiple GCs and pick the one you like best. That's basically the construction process in a nutshell.
Now, your questions:
1) Can I be more specific on materials? No, not without writing an entire novel. Windows, doors, paint, cabinets, flooring, trim, countertops, sinks, showers, etc. etc. There are hundreds of options for each. Some are good, some are bad. Do your research before choosing.
2) Do all contractors use the same materials for foundation, structure, framing, etc.? These materials are usually more or less the same and will be dictated more by your design, climate, and local building codes than anything else. More advanced options do exist (Zip Sheathing, engineered lumber, etc.), but unless you're doing a high end custom home you should probably just stick to the basics.
3) How do I translate this to a contractor so that I get what I want and they DON'T charge me an extra $50.00 sqft. and takes advantage? Don't... Translate it to your architect so they design a house that can feasibly be built within your budget, then let the contractors bid on that design. Understand that if you ask for an upgrade, the contractor is going to charge you more money so they can cover the additional labor, materials, and overhead. Kitchens and baths tend to be the most expensive upgrades, too. Remember, contractors are running a business. We're not just here to rip people off.
4) If you were me how can I structure a deal where the contractor does the construction and I hire someone else to do the finishes? Is there a way and is it worth it in your opinion? I've responded to a forum post about this question before. Take this with a grain of salt, but I don't recommend transferring responsibility from GC to owner half way through the build. If you do want to act as owner-builder, make sure you have experience with construction and a network of reliable subcontractors at your disposal. Keep in mind some cities only allow you to be owner-builder for your primary residence.