Unfortunately I don't have a save of the long reign bug, sorry. Thanks for looking into my findings. More bugs:
1. If you press the claim of a vassal who is a councilor, he will be kicked off the council and given the recently fired opinion modifiers. I noticed that in the 'make peace' menu it says that "[Your name] will become [vassal name]'s new liege," which might be why this happens.
EDIT: On a related note, if you press the claim of a vassal's vassal, on conclusion of the war he will break out of his sub-vassalege and you will be his direct liege. This seems like unintended behavior.
2. In the flavor text for the 'Crowned by the Pope' trait, it says that you are "Officially recognized" as the Holy Roman Emperor. However, any Catholic king can be crowned by the Pope. Either the flavor text is wrong or the coronation event choice ought to be limited to the HRE?
3. When you get an event from swaying a character, the opinion number listed in the event and the opinion modifier actually applied often do not match.
4. I had my crowned by the pope trait dusappear, and I'm not sure why. I'll tell the story in case it has any clues: Was playing as Duke William of Normandy. After winning the war I was crowned by the pope and the former king Harold Godwin became my subject as count of Devon. He also kept his 'crowned' trait. He was soon excomunicated and I took the opportunity to imprison him. Arrest failed and he declared war. I immediately lost my crowned trait. I wonder if it is because crowned Harold became independent temporarily due to the war between us, and our mutual crowned traits were somehow in conflict?
5. Another thing about crowns: On start, all the of-age Christian kings have the (Vanilla?) Crowned trait rather than one of the specific 'Crowned by bishop/archbishop/pope' traits. Seems like a minor oversight?
6. Balance thing: having played about 10 games from the 1066 start in the past month, with only one exception the moral authority of Catholicism is tanked to 30 or less in the first 50 years of the game, causing a chain reaction where the MA can't recover due to rebel heretic victories and rulers led astray. This is largely due to a huge negative MA from 'lost reconquest wars' which I have seen as high as -80 and and never lower than -30 by 1100.
7. In vassal obligations laws, Low Burgher obligations provide the exact same benefits as Harsh burgher obligations, but without the opinion malus. If ypu were to follow the pattern established by the other obligations laws, Medium and High burgher obligations are also wrong.
8. The decision to donate the the Hospitallers is called "donate_to_hospitallers_decision" or something like that.
9. William the Bastard's unique decision to enact primogenture in England after winning the war gives him -20,000 prestige - quite the loss. It seems like this could be intended behavior to make his vassals mad at him, but it's pretty of clunky. Or perhaps it's meant to give -2,000 prestige to be equivalent to a normal Primo law change.
10. There are several Chalcedonian bishops in England in 1066. After they die, their replacements are Catholic, so it's not a huge deal...
11. 'Groom Your Heir' Ambition won't cancel if your only son dies.
12. After a child ruler was deposed by a faction, she kept her Uncrowned trait despite now being unlanded.