Chip
I'm no expert but my first thoughts on the floor joist question, where joining a horizontal beam is that if you cut a lot of through mortises you’ll weaken this beam to the point where it won’t hold up the floor. There are formulas for figuring out how to plan the size of your floor joists and the beam necessary to hold them up. I’m not sure if these would apply to your situation but maybe you should get some more books on timber framing and do some more research on that particular section of your design. If it wasn’t done that way before there is probably a good reason why, like frame failure. One well-known author said “it’s not a re-invention of the craft of timber framing, it’s a revival.” So my advice to you is to learn the old ways that work and have worked for hundreds of years and use them. Keep it simple. As I said I’m no expert, just my opinion. Good luck on all your projects. Jim