Unit Training Classes and Equipment Levels rules are in effect. NFP troop support is not in effect.
Census rules are in effect.
Secret Empires are in existance. However, these do not represent supernatural freaks. SEs will tend more towards the politically manipulative and the Mafia more than the Cthulhu-worshippers.
When a nation is bereft of a player, I will run well-defined actions on that country, depending on the kind of leaders that country currently has. If the country has a good diplomat, expect that country to diplomacize. If it has a gifted general, expect fights to break out. They will rarely fight with player nations unless provoked, but it's not impossible. If a nation has unimpressive leaders, then the country will work on improving its economy and government.
A country can become a Super Feudal Ally of another country via a number of ways. Diplomacy and conquest are entirely possible. They can also be created by the king's fiat.
An SFA nation will pay a tithe to the parent nation, as well as offer the use of one of their leaders to the parent nation for their use.
SFAs may revolt just the same as any region of the parent nation may revolt. Much depends on the influence and past treatment of the SFA by the parent.
I am using Lorne Colmar's Lords 17 Combat rules for this campaign.