Human error aside, T4 Book 1's QSDS, T4 Book 2's SSDS, and TNE's FF&S should all match up.  I built QSDS using TNE FF&S, while Dave Golden built SSDS the same way.  We probably made some mistakes in the process, and probably also stumbled over unknown-at-the-time FF&S errata.  I wasn't involved with T4 Book 3 so I can't say for sure, but I seem to recall that it was written by Greg Porter, and probably did not use TNE FF&S as a base for everything the way QSDS and SSDS do.

Dave Golden and I were co-authors of the T4 FF&S2.  It is based on the TNE FF&S and should generally produce comparable results, except for specific cases where we attempted to fix things that were known to be broken in FF&S, or in response to specific directions from Marc and Imperium Games.  I recall that the writing and editing came down to the wire on our deadline, and we certainly would have preferred more time to review, test, and revise it.  If there is a lot of interest, I still have (most of) the files and notes behind FF&S2, so can probably answer questions about why specific changes were made.