I went through this problem last year. My first bike had a long TT and my neck and shoulders were always sore after I rode for a long time. I, too, tried to recreate the shorter TT feeling on my old bike with different stems, seatposts, and handlebars, but in the end the thing that fixed it was to simply buy a new bike with a much shorter TT.
Take my advice and just get a new bike like the Quick CX. Unless you are just trying to shave a 0.5" off, you'll only get so far with component swaps and it never really gets you where you want to go.