I'm a not particularly closet Dead fan :) and am very interested to know how your project turns out! I've long had it in mind to someday get a guitar intended to focus on those Jerryesque tones.
I had long been thinking of doing something HSS or HHS to aim between the "Alligator" strat (and '57 Fender, I believe), Jerry used a lot around '72/'73 and the HHS guitars he used a lot later on: "the Alembic through-neck "Wolf" he used a lot in the later '70s and the cocobolo/maple bodied "Tiger" of the 80s. Both those latter two used Dimarzio pups, if you can believe it! DiMarzio Super IIs humbuckers and then an SDS-1 in the neck.
Jerry used some Gibsons, though, at the end of the '60s: P90-equipped LPs and also an SG with humbuckers (on Live/Dead, for example).
So if you've got routing for humbuckers ... perhaps, yeah a Mississippi Queen would be good. especially in the neck. You could then do either another MQ in the bridge, or .... Well, I've never thought the Dimarzio pickups were that great, but anyway, the Super II is not incredibly hot and reasonably bright? I'm going to suggest the Riff Raff for the bridge, actually! Anyone have any thoughts on how that would go with a MQ in the neck? What kind of wood(s) are you using?
(If I were picking single-coils for Jerry tones ... the SDS-1 is kind of hot and ceramic, I think, but despite that I'd have to suggest Apaches or Sultans!)