This might just be typical GS behavior but....  After I've been riding on the freeway at ~65mph for an hour the bike becomes waaaaay more free revving, as if my carburetion got a lot smoother.  When I've just been riding around town it's a bit sluggish to rev up and drop revs, but after elongated freeway driving it spins up really fast.  Is this just normal?  Does it really take my GS almost an hour of freeway driving to fully warm up?

In my opinion it would warm up quicker while city riding.  Air cooled and less air flow.  Never noticed it with my '05 but it also has an oil cooler.  What weight oil your using could have an effect?  I run RotellaT 15w40.

If I rev it between 7-8k for about 15 minutes in canyons mine fully warms up. Same thing at 5500 on the freeway for 30 minutes.

You are right though- the bike runs much better fully warm.

You may want to raise your needles up one shim.

I'm using 10w-40 oil... barely uses a drop between changes.  Right now everything is stock jetting/exhaust/airbox except that I have 40 pilot jets.  I'll try shimming the needles up one, but will that cause problems with the stock exhaust configuration?

You may be lean. Air screw is my guess, as well as #4 under needle like Dgyver said and 125 mains ... and yea rejet a stock bike ... its supposed to be that way ... 40/125/1/3 is what they sent to england and canada I believe.
Cool.
Srinath.