Your choice of body/neck woods can have a real impact on the overall tone on a Thinline as well as the pickups. I built a mahogany Thinline with mahogany neck, but put hotter RG P90 pickups in it; can get a tone somewhat close to an ES-330 with the pickups set at lower volume levels.
Have not used the Lil' 59 in a Thinline, but have as bridge pickup in a couple of Strat builds. Nice vintage tone, but not quite as good as the full size SD '59s. While you've got wiring to coil tap the Lil '59, I tried that and did not like it; sounds way thin in tapped mode.
Given your PU routes you have a limited set of options; you can stick with the Lil '59 in bridge; that could balance nicely with something like a Fender Custom Shop NoCaster or Rio Grande Vintage Tallboy in the neck position,
A mahogany or rosewood neck will get you a lot closer to a Gibsony ES-335 like tone; a maple neck will be MUCH brighter, more "Fenderish".