Alan, the one thing that I've clearly learned over the past few years and recently put into action is the concept of "open space" is a good thing as it brings flexibility to the shop. I don't really see much of that in your diagrams. I've purposely created a larger open space in my shop that I can use for assembly, finishing and material support while milling and at whatever heights are appropriate for the particular function. The other thing is work flow. TS, J and P are all very closely related so having them nearby each other so you can move between them efficiently with less "material relocation" is a good thing. That's a little easier in my shop because I use a J/P combo, but certainly doable with discrete machines, too. You have a relatively large shop space so perhaps you can keep the "machining" in one area and the "building" and hand work in another through grouping. Yes, there are some tools that will need to live in other areas, but in general, that kind of configuration can be advantageous.