*nod* You may be built more on WSD lines, so it may not be possible to get the frame to perfect. Sad.
The other possibility I see is if you're using a backpack for hauling. I went for my first backpack free grocery run yesterday. With a pack, my back and shoulders are *screaming* within a mile on the way home, with the pain centered where you'd expect it for too much reach. Yesterday? no pain. This was expected, since math says the bike's reach should be fine. Plus, previous pack free rides have been fine (just not real *practical*).
I've replaced the backpack with a pair of $40 Axiom panniers. The sewing and seam taping isn't as solid as my backpack, but my backpack has lasted through 15 years of near daily 30-45lb loads. I think it's ok if the panniers don't last through that. I could have gone cheaper online or with Craigslist, but we decided "support the local bike shop" was higher priority than cheapest panniers possible.