so I just finished episode XCIX and have two to go... I thought maybe I missed a few when marathoning SJ on adult swim leading up to this, but it appears that the end of season 4 was episode 52 and the start of season 5 was episode 92 (XCII) so there aren't episodes 53 to 91.
Regarding those missing 39 episodes, are they possibly represented through the comics of Samurai Jack rather than toon eps? comicvine.gamespot.com/samurai-jack/4050-68530 has 20 issues so that would leave 19 left to account for... Perhaps the "Amulet of Time" (2003) and "Shadow of Aku" (2004) video games? I don't know if those are divided into chapters... maybe the crossovers with Powerpuff count as episodes too?