I actually posted something on AMR the other day about this issue here.
You can use AMR as a 'starter', but it's not an end all be all gospel to what you should do. Always go over it with a comb. It'll take you 99% of the way there, but maybe not 100%.
Gemming + Reforging is a REALLY complex process though, and the SP part of it needs a bit of work because it's complex as heck. Using RFL after gemming is the close to the same as using AMR and locking all your gems.











