Very familiar challenges. My neck was broken in 2001, and reinjured in 2018 when I was hit by a car, also breaking and dislocating my shoulder. Recovery took much longer than I'd have expected and it's an ongoing process. I spent a few months in physical therapy last year and continue doing PT on my own at home every day -- stretching and range of motion every day at a minimum. Body weight exercises, etc., 2-3 times a week, including kettle bell type exercises using jugs fill with water (about 20 lbs each).
Lots of massage using a long handled dual headed percussion massager, usually with some sort of topical analgesic (I like Ted's Pain Cream, and sometimes add plain ol' DMSO and some CBD balm).
It never completely stopped aching and is worse with rapid barometric pressure changes in advance of storms. But some days it's not too bad.
Padded shorts will help. Ditto good bar wrap, the foam type often referred to as "cork" although real cork is pretty rare now. I also liked Arundel Synth Gecko and similar silicone wraps that don't need adhesive and can easily be rewrapped.
Tires and tubes help a lot as well. I've switched around a bit over the years and for the past year have been pretty happy with Continental GP Classic skinwalls, which are 700x25 only. I'd go wider if I could but my old school road bikes won't take larger than 700x25.
Recently I switched one bike to latex tubes just to see if they lived up to the hype. I immediately noticed an improvement in reduction of road chatter and vibration on chipseal and rough pavement. No idea if they're really faster since I'm not particularly fast. But they are more comfortable. Pricey (around $15 each from Silca, but there are other makers) but worthwhile for the comfort for me.
I usually run tire pressure lower than I did years ago. With the Conti GP Classics and latex tubes, around 80-100 psi rear, 60-80 psi front. The ride doesn't feel any more sluggish at lower pressure so I tend to ride around 85 rear/70 front. At 150 lbs I could go lower but I'm okay with what I'm doing now. If I make any other change it'll probably be to tubeless.
I wouldn't suggest a saddle change if your bum is satisfied with your current saddle. Try padded shorts first. I did get somewhat more padded shorts and saddles after losing about 25 lbs -- less cushion around my sit bones. But it was tricky finding a saddle that suited me. So I'm reluctant to change saddles if what I'm riding seems okay. But I'm willing to change bar wraps, tires, tubes, etc.
I usually ride 20-30 miles, and about once a week do 50-75 miles. That's about my limit. Beyond 75 miles the neck and shoulder pain quickly sap all the fun out of riding, so I might do a full century once a year just for the heckuvit.