I was wondering if anyone here was familiar with Yamaha outboard motors,
specifically from the 90's, and of the 9.9 HP (although most I think are
similar)...

Here's my story, I've had my motor just over a year now (used motor), and
the previous owner who had it had a bottom end problem where he hit
something and had to replace the gearcase... so it has a new lower unit on
it. Last winter due to various circumstances I didn't check the bottom end
for water, and it ended up freezing, thus pushing out the lower case cap
(behind the prop) and breaking it where the bolts go... after getting the
new cap with various seals, etc, I've put it all back together, and tested
it in a controlled environment. During the first test after some running I
noticed the white oily sludge all over the bottom end, so I checked and sure
enough water in the oil already. So I took the gearcase off, cleaned
everything up, and then noticed that things seemed loose in the area
surrounding the shift rod that goes down right into the gear box... Loose
was a rubber boot, and this weird plastic bracket that is suppose to hold
this boot down and keep a seal to the gearcase. The bracket was just
sitting there so I assume that was the cause. I refitted the boot into the
hole (just pushes in but not very tight) and then put the bracket back in
and the screw with expands the bracket to keep it put). My next test
included leaning the motor over as I had done before where I knew oil would
leak out of those tiny holes on the case surrounding the chamber where this
boot and bracket are (above the gearcase)... This time, no oil leaked out at
all. So I started it, and ran it at idle in both forward and reverse for a
bit. With a bit more throttle I then turned it off as I noticed a bit of
white in the water. As I tilted the motor up I noticed the tiny holes from
the chamber which houses the boot, bracket, and shift rod was leaking out
white stuff...

So, I'm suspecting now without taking off the gearcase again, that this
boot, and bracket area is where the leak is coming from. At this point
except for ordering a new boot and bracket I was wondering if there were
other options to try?

One thing I considered is some silicone around this boot as it slides into
place. Surely that would hold it in, and seal it as well right?

Else I can order the new parts and put them in. But, is there anything else
that could cause this problem? Note the lower cap has all new seals and
bearing in it, so it should be fine.

Cheers
Chris