Hopefully the permatex will give you a better reading on if that is the issue. I`m from the school of fix the obvious first the two water tubes should stay in the exhaust housing when you pull the gearbox. Are the water tubes fully seated in the water pump and lower grommet on that gearbox the water pump only has one grommet on top for that setup I believe. I have been too lazy to pull my gearbox and see how it goes putting in 10+ hours a day fixing heat pumps.
I also ordered two new grommets, but actually there are two tubes coming from the water pump. And those long days will catch up to you!