Shaft Seal Replacement 99' 50HP

I'm replacing the shaft seal on a 99' 50 hp Johnson (J50PLEEA) with the gearcase full of oil, motor trimmed completely up. The repair manual says to apply a light coat of gasket sealing compound to the bearing carrier o-ring flange and aft support flange when it's inserted back into the lower unit. As I'm looking down into the gearcase, the top third of the thrust bearing is visible in the gear oil. If I slide the bearing carrier back in with the gasket sealing compound on the o-ring flange, as the repair manual states, it will end up in the gear oil. This does not sound right. Has anyone else run into this before? I was trying to save the gear oil becuse it's less than six months old and shows no signs of water intrusion. Thanks!

If there is no sign of " water intrusion ", then why are you replacing these seals ??-------I would at least drain the oil , assemble the unit.----------Then pressure test to check your work !----Then put the oil back in.

The boat had not been used in over seven years when I got it. It was left out in the elements uncovered, even had bushes growing out of it. Cleaned it up, re-built carbs, cleaned fuel pump, checked spark, replaced all hoses, etc. Ran it about half a dozen times before I noticed oil in the garage. It appeared to be coming from in front of the prop and dripping down the skeg. The oil would appear even if the engine had not run in several weeks. Whether correct or not, I assumed that the shaft seal or o-ring was bad in the bearing carrier. The o-ring looked a litle rough, but the shaft seal seemed ok. The new ones will be in tomorrow, so I'll go ahead and replace. Sounds like draining the oil will be the best way to go if gasket compound is needed.

It is quite normal for oil to leak there and it is usually the oil that is mixed with the gas.This is common when motors are run in the driveway on a hose.----------Pressure testing is done to find actual lower unit leaks.

Thanks for the reply!