I am back on a road bike after 20+ years. I have a Synapse Carbon 6.

When I started last fall my biggest issue was my elbows. It went away after about 5 rides.
I have had one seat issue. Started at around 23 miles on a charity ride. It was strange as it was not my first time at that mileage. I rode to 33 miles that day and it was not fun. I have surpassed that mileage many times since with no problem.
My neck hasn't experienced more than a tinge of mild pain here and there.
My biggest problem is that my left hand falls asleep. I keep a nice relaxed bend in my right arm but I find myself straightening my left and shrugging that shoulder. I have to concentrate to avoid this. Numbness hits around 15 miles.

Sounds like you are well conditioned but you are using some new muscle groups due to the road geometry. I would give it a couple more rides before you start making changes. I thought the elbow issue was going to require a new set of bars and then it was just gone. Poof.

My 17 year old son, who is a competitive rower, is currently getting used to his new road bike. He also skates 8+ hours most weekends. He has my elbow issue and his seat hurts. He can't get out much until rowing practice ends for the summer. We will see how he works through the issues when he can spend some real time in the saddle.

Welcome back.