I wanted to try to draw up a plan with the public spaces --living, dining, kitchen - all lined up on the north - south axis. This meant turning your kitchen into the laundry room + mudroom hallway with the hope that keeping the back door and the side window intact will save you some money. I also hoped that not fussing with that pantry addition would free up some budget as well.
LIke @palimpsest, I find all the offset walls off putting, so I aimed to give the living/dining/kitchen a common wall on at least one side. The dotted blue line just represents new cased openings to the mud "hall" and the staircase.
If the size of the current primary bedroom works for you, I say keep it and just absorb the main bath into it to create a suite. The two common walls with the office are a definite compromise, but if it's always going to be an office it shouldnt be a big deal. Planning ahead, you can have them add a second layer of drywall for added sound attenuation.
I also tried to be super mindful of the traffic flow throughout your home. And that's what the red lines are. In smaller homes you don't want to waste square footage on zig zaggy traffic patterns. And if the main bathroom is a 15 ft straight shot from the mudroom I really don't think you need a 3rd toilet (unless you decide to put one downstairs.)
Your project is a really fun puzzle and it reminds me a lot of when I worked and worked for almost a year to figure out how to optimize our remodel. It wasn't until I explored the idea of moving the kitchen all together that the final plan fell into place.
Posting just for fun and with hopes it sparks some useful ideas - even if the ideas are "no way!" :-)
Q