I'm a HUGE U2 fan, I don't know all his gear or anything but this is what I do know.
Main guitars used on Rattle And Hum (DVD):
Black Fender Stratocaster (His chime machine)
White Gibson Les Paul
I don't think his Explorer was used even once on that DVD, could've been.
ZOO TV in Sydney:
Mainly Les Paul
Some songs with Strat
some with Explorer
Vertigo Tour Chicago:
Fender Strat
Gibson Les Paul
Epiphone Elitist Sheraton
Fender Tele
Gibson SG (used only on Elevation from what I recall)
I have 4 U2 vinyl albums, one being Under A Blood Red Sky. Most of the songs on that sound like his Strat, the few that don't sound like his Explorer.
When I saw them in Toronto at the Air Canada Centre in 2005 he used his black Strat the most. I think there was another Strat as well. He used the Strat on Sunday Bloody Sunday (the Chicago DVD he used a blonde Tele). He used his SG on Elevation, a Gibson Les Paul on quite a few songs as well as the Explorer on a fair number of songs. He also used his Epi Sheraton on some of the newer songs (Crumbs, City Of Blinding Lights, All Because Of You). I believe on Sometime You Can't Make It he used the Rickenbacker, though if I'm not mistaken at the concert I was at he didn't have it in the gear set up and used a Tele.
As for the pups I'd reccomend, I think a twang banger bridge, SSL or Antiquity middle and a Cool Rails or Lil' 59 neck (for some of the Gibby tones). The precious suggestions have also been quite reasonable and are worth a shot.