@
WOT, I did many of the same things you had done, with a Trek DS. Started with a custom quality wheelset, along with fenders and rack. Altered the saddle, stem and bars to suit, plus good lighting and safety/reflector improvements. Made a much more useful, practical and comfortable ride, at the expense of being heavier than the "floor" model as delivered. A joy to ride, by comparison.
As some have suggested, finding the right "fit" for things is a process.
The wheelset I did were: Velocity Dyad 700c 36H, DT Swiss spokes, Shimano Deore XT hubs, quality build, with Conti Tour Ride 700x1.95 tires. Not a peep through years of use on rougher urban streets and mild trails. Considered a higher spoke count, being a heavier rider, but 36H was fine given the quality of the build.