You probably don't need to mention waterproofing except perhaps to say "seal joint between window sill and sub-sill with paintable silicone (or urethane, etc.) sealant. The sub-sill should extend beyond the window frame at each side far enough for the vertical jamb trim to stop against it. The siding should be installed under the sill-nosing so that the drip groove in the nosing projects beyond the surface of the siding. Sealant at the siding to sill-nosing joint might be appropriate too. Flashing would be in the flashing spec or window installation instructions. Paint would be in the painting spec. Advanced TrimWright, Inc. makes two sill profiles: standardSILL and historicSILL. Older double-hung windows had very large projecting sills which is why many of them are still functioning today and will probably be around long after a lot of modern nail-fin windows are replaced. Modern windows are intentionally designed so that the sill only projects as far as the jambs of the frame. This is easier to fabricate and also easier to put in a box for shipping. Modern window manufacturers think little about waterproofing for residential and commercial buildings, relying instead on modern sealants that must be replaced many times during the life of the window. Your goal should be to avoid that costly maintenance chore by letting water drip off of the window clear of the siding below like in the old days.

Thank you WoW (I've heard good things about you in this forum multiple times...). I understand what sister means when it comes to joists, but are you talking about adding a sloped piece of wood to fill the void, or cutting off the nose enough so you can fit a piece in vertically?

Thanks for your input! I walked around the house and did some additional investigating. I think that the entire sill is going to need to be replaced on some of the windows, so this will definitely be a "next year" project. I am concerned about possible leaking inside the windows. I'm basing that on the fact that the bathroom window (yep, window inside the tub) has mold on the bottom of it (when you raise the window, the bottom metal it normally rests on). I had the shower redone last year to replace a leaky, horrible plastic shower surround. I was heartened that the studs did not need to be removed and only had slight water damage. I also found that there was no caulking on the outside of the house on the window lip where the metal meets the siding. My friends and I caulked up there, but to be honest I failed to remove the mold at that time. I think since this is on hold right now I'm going to get some mold killing solution, spray down the window and see if the situation reappears over the winter. If it does, I'll know to expect possible bad surprises come spring!

Your trim would be easy to replace and look much cleaner to install new after the tile. I can't tell how old your windows are, but did run into a problem with my old ones. The wood under the sill was on a slope and had to add a strip of wood to mount correctly. Plus the center style couldn't be removed with two windows creating a large one. I would also remove the side trim and fit after the sill. Family Handyman has some great how tos for working with many types of windows.