What the frame thickness? I would imagine 3 1/4", and then your wall is 4 9/16" so you would need cement board returns which would need to be taped , as well as the window to cement board transition, then the whole enchilada covered with Aqua Defense. I do not know how it would possibly to do all of that after the tile was installed. Personally I would wait since you obviously cannot plan it out better at this point and this point of the waterproofing stage is crucial as you really do not want your exterior wall system getting water infiltration (insulation wet = mold = rot).

if you do install shutters I would suggest making them operable, installing shutter dogs to hold them in place and size them to fit the windows. That would be hard to do with the wider windows. I might also suggest eliminating the stone base of the porch columns and install real, solid wood columns that go all the way down to the porch. If you are going to have an arched top window where it is placed is the best place for it. The arched top window is somewhat passe and what you would expect to find in a builder grade house. Would also suggest using another garage door - one with lites (windows) at the top in some configuration. Good luck!

House stile and existing windows not being change also factor in. Tough to answer a question like that is a vanilla box with zero context.

you sure it's tucked behind? It can be on the J-channel but if its capping, its not usually nailed through. Cutting the caulking will normally free it up for removal.