Of the three door options, in my home, I'm going with the 42 inch front door. I've never been in a house with glass on the side of a front door that I liked. To me, it's a 90's fashion thing that isn't done very much anymore.
You mentioned that those windows over the front door wont be so "garish", but in your pictures, they are overpowering and very, VERY busy.
Home design, colors, and materials are just like clothing fashion, but instead of changing every year, they seem to change every decade. There are things that become popular and everyone does it, then it goes away and we all wonder what everyone was thinking. Glass tile seems to be the thing that nobody is doing anymore, but they for awhile, it was everywhere. Right now, the trend in tile is white subway, and fake marble. I think it's important to be sure to do what you really like, and run away from all the latest trends.
If it was me, and I was building your house, I would think seriously about the window in the gable on the left of the house, and those three windows above the front door. You have changed the porch and it's not so overpowering, but I think it still needs attention. What does it look like without the open gable and just extending the existing roof down over the porch area? Or maybe a maybe just a smaller gable porch that just covers the front door area?
You have one of the best floor plans that I've seen. Before you build, be sure the exterior is just as good.