The Simplified Protocol hasn't changed except for the substitution of Metagenics Actifolate for Metagenics Intrinsi/B12/Folate, and that was only because Metagenics changed their formulas and removed the critical ingredient from the Intrinsi/B12/Folate.
As far as supporting supplements other than the basic 5, everyone deals with that differently with either the help of their doctor or what their own research and body is telling them. I doubt if any two people on the Simplified Protocol are taking the same supplements other than the basic 5.
I buy everything online from the cheapest source I can find--most are available at Vitacost. It is only the Metagenics and Perque brands that are not commonly available--oh and the multi that Dr. Yasko and Rich recommend is only available from Dr. Yasko's site HolisticHeal. If you go to the Yahoo group CFS_Yasko and look in the files section you'll see a document that gives the best sources and prices for all the supplements that people are taking.