I would say that, you need to let your knees heal a little. Then tweak your set up.
Even with the best of fittings, sometimes on the road, (not the trainer) we ride and pedal a little bit differently.
I am going to guess that between the newness and the miles ridden is the cause of your discomfort.
As I said, I would mark the settings I have now and tweak with it a little at a time. This will give you time to get use to the new... gearing....cranks...whatever.
Doing a 100 mile ride with 7500 ft of climbing, I don't question your overall fitness.
Doing the right thing is always the best way to go. Even if we don't want to. IE; Hammering when we normally spin, and that is a very easy thing to do on a new bike.