The style you are describing is not Shaker, but rather more Arts & Crafts or Craftsman. The Shakers wouldn't have done something so "fancy".

I used a very similar style trim in my house and just butted it into the wall or notched it where there wasn't enough room for the full 4-1/2" wide sides or 6-1/2" wide top pieces. Some places where the ceiling was low I had to reduce the width of the top piece. Somehow it all looks OK in the end. I think it comes down to having it look like a visually obvious choice to have made about how to deal with each odd situation.

If many or most of your doors/windows have a problem then you probably need to re-think the trim.

Out of 15 doors, there are 4 that I have an issue with and they're all in the same area. I think going from a 1x4 to a 1x3 on the side rails will solve the problem.

I thought it looked better to rip the sides to the exact width of the available space (and scribe it as required to match uneven walls), rather than leave a small gap where a full width board wouldn't quite fit. YMMV.