You're describing what I believe most committed, long term commuters eventually figure out; finding the perfect bike is a process of discovery and evolution. I always advise Clydes seek out a quality wheel set at the earliest opportunity. I'm not so sure I'd recommend a 48 spoke rear, but by doing so you've just about guaranteed yourself a lifetime wheel (not counting brake track wear). And your LBS guy is correct - I have a Shimano dyno hub similar to yours and it's provided thousands of trouble free miles. Your cockpit setup isn't anything too radical.
SQ-Labs inner bar ends seem right up your alley.
Isn't is nice when you get your bike dialed in just the way you like? It's good that you've posted your experience as it could be a big help for others trying to find their own solutions.
-Kedosto