Just looking, the Brooks saddle might need tilting up a smidge. I also like having the hoods on my bars the same as you originally had them. Machka has hers even further up.

If you feel uncomfortable after such a short distance, there might be fundamental issues, but if your fitter said it needed several hundred miles to get used to, then there certainly is a probelm with his philosophy.

What recommended this fitter to you?

You also should be making very, very small (as in 1/16th inch/millimetre) alterations to your fit as you ride along in the first hundred miles or so. IF you are reasonably satisfied with the way other aspects of your fit work, then try tilting the handlebars back towarrds you a few degrees until you find a "sweet spot". The same with the saddle. You may even find that when the saddle is fully broken in you may have to lift it a millmetre or two to compensate for the divots formed by your sitbones.

Naturally, working on core strength is needed for long rides and it exercises to increase it certainly don't go astray. Moving the seat back may have accentuated any weakness, but really, it shouldn't require you to push back on the bars llke that.