If you didnt overrev the engine or run it low on oil i think its possible the previous owner might have.
A 2002 jeep engine with only 40k on it, must have came from a wrecked jeep with serious damage.
Second, never buy a mechanic's personal vehicle. its the one that never gets fixed right.
88 YJ, 4.2 5spd, Hardtop, 6" Skyjacker Monoleaf, 33's on alloy, RockCrawler Bumpers, Tube fenders, Full wrap body armour, 4.88's, SYE W/CV.