Wraith CrystalGlum Reaper's flag is above the center crossbar of the Forked Crystal puzzle, where the wily mouse cursor will find an invisible letter B.
Vomer's flag is formed by a set of spooky, mostly monochrome emoji in the Peril Crystal puzzle. (If you happen to include the jack-o-lantern because it's so macabre, all you end up with is a wonky A.)
Li'l Boo's flag is on the main page for this round of puzzles. Mouseover Culex's chest to reveal the letter R.
Straw Head's flag is in the Epistle Crystal puzzle, in Wicked Woods. The hands of the clock tower face form a semaphore E.
Box Boy's flag is in the Vault Crystal puzzle. The floor plan of Kopr's dungeon (the first one) forms a letter L.
Shaman's flag is in the Stalking Crystal puzzle. The "red face" (Bowser space) that's right outside an eye door ends up having a Y on it in the solution.
The answer is BARELY.