This is a great case study, thanks for taking the time to post and update it! I have been lurking on it since you posted it, waiting for updates. Hopefully you will keep it going.
To answer your question personally I use rank tracker to monitor rankings of my money sites, PBN sites, and web 2's. It has a nifty keyword suggestion tool for KW research in it as well, but isnt free or cheap even (depending on what cheap means to you). Serp book would also work for monitoring your rankings if you already know all your KW's and can afford the monthly bill.