Hi guys,
I recently picked up a Danelectro Longhorn reissue from the original Korean batch. It's a "Pro" model so it has the adjustable bridge, but even with the saddle all the way back my E string is still about 5-7 cents sharp at the 12th fret. I love the way it sounds, but my love of its vintage charm doesn't really extend to playing an out of tune instrument if I can help it

. I have some experience setting up my instruments, but I'd welcome any advice. Here are a couple of questions:
1) Assuming I can do this while still making the bass playable, am I correct in thinking I can help by raising the bridge and then compensating by tightening the truss rod? My theory is that this will lengthen the string from the bridge to the nut, so the spot where the saddle needs to be will also move forward and (hopefully) to where I can set the saddle correctly.
2) How would changing strings affect the intonation? It currently has D'addario Chrome 100's, which I think is the heaviest gauge the tuners can accept without being modified. I'd like to stick with flatwounds, but I know other brands can have different tension. Assuming I adjusted the truss rod to compensate for the different tension, would that tension affect intonation, and if so, would I want to go heavier or lighter?
Thanks for the help. I'm going to play around with it this weekend, but I'd like to have an idea of what I'm doing so I don't have to remove the neck to adjust the truss rod more than I have to !