My first thought on reading your original post was "Oh man, landlocked, your ear is in for a world of hurt."
I think anyone coming from the world of pro-level orchestral brass or strings playing whose ear is sensitive enough to discern just-intonated chords from equal-tempered chords could well be shocked by how poor the tuning standards are for fretted instruments.
Even the highest quality guitars are far from achieving the equal-tempered tuning accuracy of a keyboard instrument, never mind the pure intervals you're used to.
There are technical innovations in fretted instrument design which help this issue. I'd highly recommend getting a guitar with the Buzz Feiten
modification or having the mod done to your guitar. This mod tries to bring the guitar closer to the tuning of a stretch-tuned piano and both of my guitars which have this(one electric and one classical) sound immensely more in tune all over the neck.
The True Temperament
system also tries to bring the guitar closer to keyboard accuracy of tuning. Their solution of creating crooked frets but not using a compensated or intonation-adjustable nut makes no sense to me but I've never had a chance to try one so my opinion is not terribly valuable.
One of the most elegant methods for improving fretted tuning accuracy has been developed by Gary Magliari
which he did an excellent presentation on at the last Guild of American Luthiers convention.
Unfortunately there's not much info published on the web yet but his presentation will probably appear soon in one of the upcoming American Luthiery magazines.
His approach involves compensating at both the bridge and the nut, and then tweaking the scale lengths of each string so that the frets become straight lines again instead of remaining crooked like the True Temperament solution.
I'm just completing an acoustic steel-string with Gary's system and I'll try to post again when I've had a chance to play it and take measurements with a strobe tuner.