Have you checked unhappiness inside city screen? If it states 0, something is wrong, because rarely you will have 0 happiness. If it's something different, you can see what is causing unhappiness there, and it's just a problem with display as pandasnail says.
I always install the EUI version and check all 6 mods.
Just guessing, it can be that you are suffering urbanization unhappiness, for having too many specialists.
From the city screen? Not seeing a separate happiness field there (the happiness hover is also on the main screen.)
Not urban unhappiness with only 2 specialists within the empire. I also had verified that total wasn't changing.
The other weird thing is Happiness : From difficulty level is now a few points higher than it was earlier.
It may be the case that #2 requires #6 to see this properly (even though it's not listed anywhere in #2 .modinfo file); could also be the cause of the cultural screen overview being weird.
Screen shots attached (from later in the same game than above one)
As to why in that screenshot happiness was -1; at the time two negative events struck that pillaged improvements struck in close succession (flood -> pillaged 3 farms; mine collapse -> pillaged a mine), I was working to repair them as fast as possible given where my workers were at the time. I think during the above screenshots one of the farms had been repaired but the other were still being repaired.
I'd like some advice on micromanaging my cities, particularly manually selecting specialists.
How do you decide which building to manually work? Do you have them all on, and permanently? Do you just work them until the point it's hurting you in city growth?
I'm still trying this out myself; but the moment I built Marketplaces I had no choice but to have every city run a merchant specialist for awhile to prevent having units forcibly disbanded on my start. (Lots of Wine; 1 Silver)
I was actually glad to discover that building a Lighthouse granted 1 gold in all coastal tiles since it let me fire them quickly enough to avoid accidentally spawning a Great Merchant. (Cash was such a major problem that I had my capital building units just to disband them for cash for ten turns)
I also wanted some more culture to get thru Tradition faster and so I ran Court Chapel long enough to spawn a Great Artist.
Correct. Mostly you would only use Specialists to balance out the unhappiness problems. Too illiterate/bored? We need some scientists!
That would explain why earlier when I had my capital run a merchant for a few turns that happiness was 1 point higher than either running a scientist or not running a specialist.