Intake/Exhaust Gasket Help

I would suspect you exhaust manifold has warped due to heat cycling and is just stress relieved and moved. So having the flange ground flat again would be a good idea, IMHO. And if your stainless nuts are staying good and loose, maybe they are just back off. Try regular steel nuts with anti-seize made for heat, or brass.

And yes on the 160 t'stat beling low; the front cylinders on inline 6's tend to run cold and the #1 bores will wear more than the rest, and the lower temp t'stat is just causing more cylinder bore wear, amongst other things.