Wow lots of replies last night while I was in bed!
First, the red cheeks issue -- Pepti Junior is a hydrolysate formula...as in, the milk protein is broken down so that milk allergic/intolerant babies can have it. So, the doctor who prescribed it at least suspected that Caleb was milk allergic or intolerant (minor difference between allergy and intolerance, is like splitting hairs and doesn't really make a difference at this point which it is...) I know from another thread of yours that he had mashed potatoes with milk, butter and cheese in them the other day - and so I suspect that the red cheeks are a reaction to the dairy from that. It could just have taken a couple of days to work through his system, and the red cheeks are either a skin reaction or a really bad tummy ache that is showing itself in red cheeks (have no idea WHY tummy aches show up as red cheeks, but they do!)
It could also be some of the sleep issues you are having - the screaming, the not going down, the waking, and so on. If his tummy is upset then it can create havoc on sleep. My DS didn't sleep more than 30 mintues in the day and a 2 hour stretch at once at night from BIRTH to 4 months when we finally got him off of milk! So, when you say that since you started dropping the CN, lots of other issues have come into play, I would look at some of them as coincidence or isolated - not related to dropping the CN but just happened at that time and the two (or three) things interfered with each other and made things appear worse, iygwim.
I found that at that age, the screaming before bed (or nap) was a "not want to sleep" cry. Used to drive me bonkers that I could do wind down, which he KNEW meant sleep, swaddle him, carry him up to his room and he'd be fine with it. But the second we neared his cot, it was bloody murder! I used to think "you KNOW this is what's coming, why not tell me BEFORE now!" Sigh.
One thing that I found helped me (and still does) when we get into these binds is tossing A time and EASY out the window. Keep feeds at the same time every day, but let him sleep when he will sleep and not sleep when he doesn't want to. Being out as much as possible during the day helped me with that (as in, letting him fall asleep in the car or pram when and for as long as he wanted to). For two or three days. Keep bed and wake consistent even if it means setting your alarm clock for 545am (groan).
Then, plot everything out in a nice chart so I can see how it looked. If he slept at the same time every day, it could be a natural biorhythm. If he slept short naps after 3 hours A time, then it could be I need to move to 3h15m...and so on. But I'm a "charty" person and I was convinced that I could use logic and reasoning with a 6 month old baby LOL! Although, I have to say, by 10/11 months it had paid off....I was able to see things stand out and play with them teensy bits every few days to get things where I wanted them.
It could be that you may need to start doing things a bit more by the clock, too....by 8 months I started going a bit more on "set" naps rather than A time. So, nap is at 930 every day no matter what. (Give or take 10 minutes, can't force a baby to sleep or keep a tired baby awake), but it helped him know what was going on. If he slept until 7am, well, nap was still at 930, and he would be tired by then anyway, his internal clock told him to be. If he woke at 6am, well, tough beans Mr, nap is at 930! Although, I would probably have moved it to 9am in that case, but still keep it a bit more by the book. It helped to get a morning nap set and consistent and then I have just either shortened or lengthened it and adjusted the pm nap as needed. It means that at 13 months now, DS still has his morning nap at 930 and we have just cut it over the months down bit by bit as the pm nap went wonky, and moved the pm nap earlier. It was a long process (as everything is!) to get here, and to get onto "set" naps, but it helped both he and I know what was coming at certain times of the day. Something to possibly think about...
But, until his cheeks clear up I would be tempted to be a bit less worried about what's going on with sleep (as in A times) and let his tummy settle.
HTH?