Hollow Knight's 112% is fifteen categories: 14 bosses, 7 warrior dreams, the 3 Colosseum trials, 36 base-game charms, 7 pieces of equipment at 2% each, 3 spells at 1% per level, 3 nail arts, 4 masks, 3 soul vessels, 4 nail upgrades, the Dream Nail with its awakening and the Seer, the 3 Dreamers, the Grimm Troupe, the Hive Knight and Godhome. The checklist keeps all of them, with what each one is worth.
Tick it by hand, or import your save and let it tick itself; if you follow the file, it catches up at every bench. The collectibles that add no percentage but do add health and soul (46 grubs, 16 Mask Shards, 9 Vessel Fragments, 6 Pale Ore and 8 charm notches) are on the Map, each one in its room.
Six points from the last two updates: the Hive Knight (Lifeblood) and Godhome's five (Godmaster): the Godtuner and the first four pantheons.
No: neither grubs, the Hunter's Journal nor the maps do. The charms the Grubfather gives you do.
Almost nothing. The delicate one is the Grimm Troupe: the Nightmare King and the banishment count the same, but you pick one.