1) Currently, to arrive at the average, you're dividing by two instead of by 3.
2) I don't understand your points column. I usually scale the rankings to a common base (ie 100), add in a variable for players who don't appear on the list (usually 150), sum them up, and give them a score based on reverse rankings.
3) Add a binary column to distinguish between players that have already played, and those that have never played in MLB.
4) This looks like a lot of work. It's easier to just copy/paste the lists (format the extras out) and then do a lookup table.
5) You may want to consider giving different top 100 lists different weightings.
6) You could add Prospect 361. They're not huge, but they focus exclusively on milb. Not sure about KATOH.
This is awesome though. I'm going to export this to Excel to do my prospect rankings.