Based on this (and your photos) your saddle is a couple inches too low. You leg/knee should only be slightly bent at the bottom of the pedal stroke. A good starting point for saddle height is to place your heel on the pedal at the bottom of the stroke, and make sure your leg is perfectly straight (with heel on pedal). I find that method gets you pretty close to saddle height- and if anything you might need to raise it about 1 cm from there.

Having the wrong saddle height will guarantee that the bike is not comfortable. But, there are other things to consider. For example, getting your body used to riding is the other 50% of bicycle comfort. Most people neglect this part and expect to be perfectly comfortable riding right off the bat. This may be possible with upright, city-style bikes, but not for long distances and rides of over an hour. A good touring bike will not be fully comfortable until your legs and other riding muscles (including your behind) are stronger from riding.

Nice bike by the way.

+1 on padded gloves

+1 on getting the right saddle height set up

+1 on raising the handlebars. these Nashbar quill stems work great for that: https://www.nashbar.com/bikes/SearchD...=comfort+quill

Nitto Technomic stems are also great and look more period correct but they cost more. The removable face plate of the nashbar ones can help when you're dialing in the fit if you get a few different stem lengths.