Regarding versioning i use similar to what Craig described but i add one more digit so it is 1.0.0 and the increments are based on the following:
Major i increment the digit to the left
Minor increment the digit in the middle
modification increment the digit to the right
this is what mainly is used in programming, the funny thing that after some time you will end up with huge pile of versions that are useless mainly the ones that has changes on the right digit (mainly due to mistakes) so to be honest i do not know anyway of doing this properly without lots of clutter.
recently i was thinking of keeping the most recent version and delete all the remaining and just to keep good documentation for the strategy with the modifications and their impact and why i moved from 1.0.0 to 2.0.0 and the other details regarding the performance. there are two ways to do it soft copies you can use any software from MS Word, evernote, MS Onenote, .. huge list so you can attach your old afl files and performance files over there and delete them from your hard disc.
the other option is hard copies.
honestly i am lazy to do both