Mike,
I'll throw my .03¢ in as I converted my RF31.
Dc servo size- YEP, bigger is better in most instances. My first servos were kind of wimpy and I could not achieve any reasonable rapids with them. In conversation with Mr. Gecko, he pointed out that I was running out of steam and if a flea landed on the table, it would fault out! Be careful about the "max torque" ratings, you don't want to design to those! Again Mariss gave me some formulas to go by for proper sizing of the servo/reduction ratios to use. Everything is a trade off. Higher reductions give more torque but can limit the rapids. Plan ahead for what your trying to do. Loads milling plastic are most likely a lot less than milling hardened steel.
Timing pulley ratio- see comment above, this is a trade off type of situation. Again what loads, speeds etc do you want to achieve.
Encoders – (One moment while I put on my asbestos suit)! OK, got it on. When I first set my machine up, I used 1000 line encoders on the ballscrew and it worked beautifully. I read the stuff on this and other sites where the max was 500 line encoders. Again, it depends on where they are mounted, (if on the servo then belt reduction makes a difference) and how fast you want to go. It also depends on how fast your computer can output steps! More tradeoffs!
Internal Z axis mount – Sorry can't help with this one.
Front mount Z axis - This is one I still have a problem with. The further out your "moment" arm is to drive the quill up and down, the more you have to worry about flex in the system. We all know about the backlash in the pinion drive system so again, trade off in type of system. If you make some sort of disconnect, you introduce another possible weak link.
Wipers- I used to have a link to how somebody else did it, but here is link to my page that will give you another idea on how I did it:
Page not found – BellSouth Personal Web Pages
Lubrication – My solution was to install a one-shot system to lube not only the ball nuts, ways, and the bearings. I use way oil in the system. I realize some will say grease for the nuts, but I figure that oil on a regular basis is better than grease only once in a while (remember, you have to get to them!)