Pine is a difficult wood to stain under the best of situations. Pine has areas of different density, color, and resin (pitch) content. Using a product like Minwax prestain helps a bit. Follow the timing instructions carefully when using a pre-treatment. Little tips: i like to apply a liberal coat of oil based stain with a sponge brush. Let it set a few minutes, then rub it in and evenly distribute with a lint free rag. As one rag becomes saturated with stain, I use a second drier rag to finish the rub in. The wetter rag is great for distributing the color. You don't want any really wet stain remaining on your wood after the rub in. Once you get to the urethane, sand lightly between each coat with 220 grit paper to remove any dust bumps. Remove all sanding dust with a slightly damp cloth, let it dry and apply next coat. Again, I prefer a good grade sponge brush, but a good grade regular brush for oil/urethane works good for appling the urethane. Remember, thin coats, and sand between each coat.
First, handle drainage. If you want to install a sump pump, perimeter drain, or water proof the walls, now is the time to do that. You should also install any plumbing drain lines at this point.
Next, framing. Concrete transmits moisture, so use pressure treated, and a styrofoam underlay that would normally go under the sill plate, to keep the walls dry. With pressure treated wood, you need galvanized nails to avoid a chemical reaction that would eat a normal nail. Make sure the framing is designed for the drywall (16" OC studs, nailing edge in the corners and around the ceiling perimeter). And make sure the walls are positioned/sized for any plumbing or other utility lines. For exterior walls, the thicker the wall (2x6 instead of 2x4) the more insulation you can include.
At this point, utilities go in, including plumbing, electrical, hvac, and communications. I'm a strong believer in conduit for running communications lines (like ethernet, catv, and phone) so that you can upgrade those without opening the walls or running wires all over the floor. Note that with more outlets, you will need more circuits, and copper isn't cheap.
Insulation is done after all the utilities are finished. If you have water proofed the walls, then I don't have much against the standard fiberglass insulation. Actually, I like fiberglass because it's easy to work with as a DIYer, relatively cheap, and replacing a piece or temporarily moving it (e.g. in the attic) is simple. However, with moisture concerns, or if you live in a northern climate with harsh winters, then I'd favor the spray foam. The spray foam has the downside of being difficult (impossible?) to remove, but it functions as a vapor barrier and leaves no cracks that air can get around.
After this, you have drywall, paint, doors and trim, and touch-up paint. I like to paint the walls and trim separately so there's less work on edging.
As for the flooring, you would usually do this before or after the trim. With hardwood, you would often do the flooring first, and then the trim goes up tight against it. With carpeting, you would install your trim 1/2" above the floor and the carpet installers would install the carpet right under that.
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Most wood finishes are food safe (for table tops - not necessarily for food preparation) once they've dried. For durability you might want to consider polyurethane, but I don't care much for its appearance. Otherwise, I would just stain (or not) and use Watco oil then put several coats of a high quality paste wax such as Briwax or Mylands. There really is a huge difference between those waxes and the mass-market ones.
For most cleaning just use a very, very slightly dampened lint-free cloth (rather than a furniture spray).