Re: Wainscot molding transition
What three pieces of molding are you using? If it's just a 1x3 with basic apron, simply square cut and hold the trim back from the windows/med cabinet a little bit. If you're using a crown molding under the shelf, then hold them back from the obstacles a bit and return them to the wall.
Google "window apron" and you'll see examples of both methods, obviously, you're doing a shelf and not window apron, but the same still applies to what you're doing.
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