Hello and welcome to BW forums

When he starts screaming at wind down he could be saying he is not yet ready to sleep, or that he needs to sleep sooner, or that he doesn't like the book or routine of the wind down. It's not easy to know which it is but you can experiment a bit with timing and switching your wind down routine. I think I'd try a wind down similar to what you were doing previously rather than the book if that's triggering his crying.
When you shush/pat in arms you can initially shush/pat all the way to sleep, see if you can do it near the cot, and then continue to shush/pat as you lay him down and keep on going with the shush/pat until he is in a deep sleep in the cot. Chances are even when he is asleep in your arms he will stir as you lay him down, that's expected, keep patting and keep reassuring him that you are there. You might need to continue right through the nap at first, then as things calm down more you can begin to pat a little less each time.
I wouldn't continue with the process for 1.5 hrs, he is likely exhausted and too worked up by the crying to get to sleep by then, we usually suggest 45 mins and then take LO out to do something else. Of course if he is close to sleep at 45 mins you can continue a bit longer to see if he'll go off.
The BW methods are not cry-free methods, but you always stay with LO and the idea is to try to reassure LO that you are still there and show him the way to sleep, gradually getting that sleep in the cot.
You could also try for one cot-nap per day and do the others in the sling if that's what he is used to, it would give you both a break. To avoid confusion you would do the same nap each day so the habit is built.
With the nights, it is normal for a LO this age to need 2 night feeds or even more.
I know it sounds silly but I find him smiling less at me since this has started and I worry it’s damaging him or our relationship.
It doesn't sound silly at all. You can talk to him about how you feel, let him know you are trying this new way for sleep because you both need a good rest. When my DS was little I sometimes took him for his nap too early and he would scream blue murder, I just said "oh dear looks like I got it wrong, sorry, let's go for another play and try again later" he usually stop screaming the moment we left the bedroom and would be more ready for sleep 15 mins or so later. We don't have to be perfect parents. Your LO knows you are trying your best for him.