Thanks guys.
I sat down with the guitar today and checked some of the things you mentioned.
No bubble or warping noticed in the top.
The strings are sharp on the 12th fret on most. I tried playing notes as light as possible while still getting a good sound. It did bring the note closer to being in-tune. I don't know where I should make the adjustment, at the saddle or the nut.
E is 10 cents sharp at 12th
A is 20 cents sharp at 12th
D is 10 cents sharp at 12th
G is 20 cents sharp at 12th
B is 20 cents sharp at 12th
E is 10 cents sharp at 12th
I check each string at each 1/2 step till 12th. Most are in-tune, some are 10 to 20 cents sharp, and a few actually look 10 to 20 cents flat. You're right that the sound isn't "off" for most of my playing. I'm a perfectionist though, and interested in lutherie. Any advice on things that might help are appreciated. (Although I am sticking to the coated 11's)