I like the idea of yellow handlebar tape and wrap the ends using brown or black waxed twine plus add yellow brake/derailleur cables. Is that a leather saddle (hard to tell)? If it is, proofide it to revive the leather. Otherwise you can get a Brooks or an inexpensive but still nice Origin 8 classic saddle. I think brown will look friggin sweet. The scratches on the rear of chainstay can be touched up with nail polish. Take a pic on your phone and go to WalMart or Target and pick three 3 or 4 colors that are really close. Return the bottles that didn't match for a refund. I would also put Kool Stop salmon brake pads. Besides the nice color they will also improve your braking performance immensely. Other accessories you might consider is a saddle bag; Honjo or Woody fenders are expensive but they will add TONS of style. No water bottle cage? Get a handmade stainless steel one from King Cage. I personally like their retro Iris cage.

Don't forget to remove the plastic pie plate!