Yes the permatex will work just fine on the shank of the head bolts that go in a water jacket.
Head gaskets go on dry. It may have a top and bottom so look in the gasket
89 2.5 TBI, 4" RC lift, 1" Booms, SYE, Adams Driveshafts front and rear, Ford 8.8 with 4:88s, BFG 33X12.50X15, and a ton of other stuff.
AF Jeep Club Tail Number 184