I also am a big Jerry and Gilmour guy. I have a Twin with 2 Beyma Liberty's. I have a Jer guitar and a Gilmour guitar.
I had the EMG DG-120 system in my strat but recently changed to custom shop 54's. I also have a piezo bridge (which works really well for later Gilmour stuff (Division bell).
When I think of Gilmour a few tones come to mind. A clean Neck strat tone (think end solo in Echo's on Pompei-Shine on intro). No effects just good reverb. I also think of super reverb and fuzzy distortion. Big muff is a good place to start for Gilmour distortion (echos solo, Time solo). I have a Tone Bone tube distortion peddle that's super nice for Gilmour distortion.
You can check out
http://www.gilmourish.com/ for anything and everything Gilmour. I mean literally every gear aspect.
Party on