Which Bob? *** **** or Bob Ryley? Are you wanting the cuban architect? He is busy with his shows or chasing Martha. They don't help us out much.
I don't really picture what you have but any spaces left over after going to a smaller window may have required additional 2by4 studding and bracing put in for nailing/screwing purposes and then covered with your wallboard with taping and mudding of the joints with drywall mud. If you are concerned about waterproofing, then you should have used concrete backer board and tape and mud the seams with thinset. The entire wall should have been ready to go before tiling. I hope you don't have to tear it all off to fix the wall.
If the window jambs are narrower than the thickness of the wall then they have to be extended by ripping some similar wood to fit. What are the 1" to 2" holes from? Good luck.