Hi Bill,
All 5 manifold stud holes on the F134 motor penetrate the water jacket.
Most folks use permatex sealer on the studs.
Paragraph E102 on page 85 of the Willys Jeep Universal Service Manual describes the manifold installation procedure with torque specs.
Here's a link to that service manual if it helps (it's a large file, manual is 281 pages):
http://48cj2a.com/images/manuals/UniversalServiceManualForJeepVehicles.pdfYes, if any are stripped out, a helicoil is a pretty good fix.
Good luck!