1) I assume over the course of the season errors and minus plays are worth the same and that they are all worth +/- .67 runs. I'm sure my research was crude by a statisticians standards, but I believe it's good enough for govt work. I doubt you'll find anyone who would place the value less than .5 or more than .75.
2) I am assuming the IFA's rating's, in a neutral park, will translate to approx .675 OPS - compare players with similar ratings and I think you'll find that's pretty close. If you then look at lots of samples of .675 OPS (independent of SB) you'll find the RC's usually come pretty close to PA's.
3) I simply pulled the IFA salary estimates from will's estimates - they seemed reasonable in my own experience. As for ML experience, assuming first promotion after 20 days, the first 4 yrs should cost about $1.4M - so maybe I rounded a bit aggressively - call it $11M-$12M each between signing bonus and first 4 yrs of ML salary.
4) I compared him to Eaton. I do not characterize him as playing "out of position", he's below avg defensively but worth the trade off because of his bat. There are scads of SS's with his below avg defense and a much worse bat. I only grabbed him because he won Silver Slugger in that league and thought he pretty well made my point that you can't just wave a hand and say the guy plays good defense or not - you have to make some attempt to quantify the trade off. I completely understand Eaton's owner playing him at SS, but if it were me, I would compare "net contribution" of Eaton at SS and my best 3B choice to Eaton at 3B and my best SS choice. The answer might not be obvious.
Fungible - I don't know what your leagues look like, but in my experience, that number for a full time SS is uncommon.
RC - I simply pull it from stats pages - look under the Extended option