Two Strats will always sound different, even with all parts 'identical'. I wonder if there were ever two Strats that DO sound the same?? From my eperience most important is the wood. And not only the kind of wood but the individual piece. When I started in the 70ies I also was sure I just had to exchange pickups... wrong, s I had to find out some $$$ later Your two guitars should have the same sound difference when played unplugged.