The only thing I would add, is that I would use full-extension guides and get them as deep as your cabinets will allow.
Also, since this is a custom set-up, you are not locked into any specific height with them. Set the working height to you, rather than some accepted standard of kitchen cabinets. This way you can match the height of things like your tablesaw for an out-feed unit or your assembly area at a better height for your body.
Uppers are a rather debatable thing. Some like them fairly low to access everything in them and even use the top as a secondary storage area. Others put them higher to have more clearance from the countertop, making the highest internal shelves into the (harder to reach) secondary storage.