I'm not sure if this is how you are supposed to do it but as I'm framing my basement in presently I am putting the studs flush with the 2x4's that I put inside the concrete opening (my rough opening) Later I will put the finish trim in with shims so that It matches up with my windows. But I also have aluminum clad wood windows, in your picture you have the vinyl windows, is that a gap between the face of the window and the concrete? I think you could probably do it any way you want to.
As for the water pipe, I would try to make the seam of your sill and top plates be where the water pipe is, and then just leave that small area where your top plate is open, Or you could possibly un-sweat the fitting up top and move it up and through the floor joist, then you would only have the one pipe going up through the top plate.
are you dropping the ceiling or just putting sheetrock on the existing floor joists?
I'm sure you'll get more opinions and options. Good luck
As for linking pictures Up to the thread, I personally use photobucket.com and then put the picture in using the links that they have for you to copy under the picture. just remember to downsize the picture so it isn't such high resolution.