IMO it's the whole package. Of course it's hard to say for certain without swapping the pickups between guitars. :hee
Just for fun, here's a little comparison I did a while back.
'07 R9, upgraded pickups & electronics (Mike Turk's "MGL wind")
One of the most resonant & nice-sounding Historics I've ever played...
http://www.soundclick.com/bands/page_songInfo.cfm?bandID=939428&songID=7789813
'52/'59 conversion & retop, PAFs and vintage wiring harness, all vintage parts
One of the most resonant and beautiful-sounding GUITARS I've ever played...
http://www.soundclick.com/bands/page_songInfo.cfm?bandID=939428&songID=7789815
And, just for the heck of it, the prototype Johan Gustavsson Bluesmaster, with a custom-wound set of Seymour Duncans.
http://www.soundclick.com/bands/page_songInfo.cfm?bandID=939428&songID=7789814
All clips played through a '55 Deluxe, recorded with a Sony PCM-D50. Went through all three pickup settings and did my best to do the "same thing" each take.