Depends on lot on what you like and your budget also. Sounds like you've been around the block a few times. I'm pretty much against the idea of a do-it-all. The perfect touring bike won't be the perfect road bike, etc. So what compromises are you willing to make? or no compromises at all? Tweeking what you've got sounds good, different hbar, maybe different rear wheels for commuting and touring. Certainly the cheapest route. Is weight a big issue?
I bought a 15-25 cassette for the Katy Trail, might be real nice for commuting also. I really like my Trek 920 with brifters. You might take a look at that.
A Ti Lyndsky for commuting would be super, also super expensive. A Calfee tourer? Probly not either. A lot of "Adverture bikes " now. Would be good for commuting and light touring. Not much out there for heavy touring, outside of Co-motion? No perfect answer, my opinion doesn't count for your riding.
And speaking of, What about the Co-motion Deusche?