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.
Best Answer
Were those two situations in my house, I'd do this, respectively:
Repair the drywall and finish it. Install a chrome cleanout cover at the appropriate location as a marker using a scrap of wood spanning a small hole as the anchor for the cover screw. If you ever need to actually use the cleanout, you can cut in an access panel. No need for such a large eyesore if not needed.
Invert the cleanout plug, then install a chrome cleanout cover. You can drill right into the plug lug for the cover screw.
I wouldn't bother with spray foam or other drastic solutions to the airflow problem. The cleanout covers will seal fairly well, and if there's that much airflow, one foam plug in one wall cavity doesn't solve anything anyway.