OK, we have enough similarities that I might be able to be helpful.
I started lifting at 36 when I was 6' and 156lbs. My job is sedentary as well. I come from an endurance athlete background so I had no real muscle to speak of. I did SS for the first 9 months and it worked, but within certain limitations.
What worked: Starting Strength, but ignore everything Rippetoe has to say about nutrition. His programming will work for anyone, but his nutrition info (GOMAD and gain 30lbs in 3 months) is definitely geared towards young men. Also, do arms. And shoulders. Work on creating size by increasing your width (shoulders) and increasing the difference between your width and your waist. Eat protein.
Don't bulk. Don't even think of bulking. You can not force-feed muscle at age 40. In fact, stay leaner than ever. You don't have the luxury of a young persons metabolism anymore. Nor do you have the time to go through endless bulk/cut cycles.
Read EyeDentist's thread in B,S,L.
Read everything you can by Dan John.
Experiment, but be smart about it. 3 weeks isn't enough time to determine anything. I've been doing high pulls for 5 months and just noticed the first bit of trap development. Which is good, because I was going to drop them in another month. I give everything 6 months.
Work on shoulder stability. Can you do laterals? Deadlifts? Rows? Get a referral for PT from your doc if you don't feel comfortable programming shoulder stuff on your own.
When you plateau doing SS, bump up your cals by 200 a day and keep going for another month. Don't mistake short-term lulls for stagnation; progress isn't linear.
Keep running if it keeps you sane. Add some hill sprints or sandbag carries. Walk around a track holding something unstable overhead, I've used my daughter. It's extra incentive not to drop the weight.
Don't diet. Don't get fat so you don't need to diet. Being sedentary and trying to diet is like being in some kind of death spiral.
Edit: do the things that give you external validation; it feels good. I like numbers so I get DEXA scans and bloodwork twice a year. If banging out 20 sets of curls a week makes the cute girl at the UPS store comment about the way you look in a T-shirt then go for it. It's your life and your goals.
Value quality of movement. Play frisbee on a beach, try yoga, try kettlebells, hike, but keep moving. Sitting will kill you, sitting is the new smoking.