For the head gasket, I don't believe there are any that require use of permatex. Felpro is probably the most accessible gasket, but it is actually slightly thicker(.053") than the OEM gasket(.052), thus lowering your compression ratio a hair. I would recommend the Mopar performance head gasket since it is slightly thinner(.043") than stock and will boost your C.R slightly.
If you have the time to remove the engine, maybe you'd want to strip it down to the bare block to have it professionally cleaned. I don't know what else to tell you about the cooling system. Has the engine sat for an extended period of time where there was a chance for rust to form?
99 XJ Cherokee, 2 door, 4.6L Stroker, 5 speed, 4x4, 8.25" rear, 3.07 gears