I purchased an Fx3 about 2 years ago. The first adjustment was the saddle which improved my comfort quite a bit. The one that came with the bike didn’t agree with me. After riding it for a little over a year (which I enjoyed), I took it to another Trek dealer and he put me on the bike attached to a trainer. He had me spin a little and made some measurements. He adjusted my saddle back a little and added some height to my stem since my hands would go somewhat numb. This helped with less pressure on my hands and all but eliminated the numbness.

I would check with your LBS and see if they can do a follow up fitting/adjustment now that you have a few miles on the bike. It was surprising to find how much these seemingly subtle adjustments can improve the ride.