Looking for some reassurance/advice

take your time, and while you have everything apart inspect the rest. when the 3.73's were put in were the carrier bearings replaced? if not i would replace while it is apart.

With 128k miles on the original rear end, may I suggest you rebuild it entirely if you're planning on driving the car hard and keeping it for a long time?

My 155k 02 GT's pinion seal is leaking and I am considering rebuilding the whole rear end. More likely, I will source the parts and get a good price and then hire someone to do the job.

when i did the 8.8 in my truck, i bought an install kit which included all the bearings and shims for everything in the diff. this DID NOT come with axle seals and bearings. also i replaced my carrier with a new ford racing unit (burnouts with 35's=broken parts) i would look into a rebuild kit for the diff also. With your miles I would plan on an entire rebuild. Do it once and be done!

Ok your first issue the rear pinion seal.
First you jack an secure your car up.
Second take your driveshaft loose an out. Four 12point bolts. Think they are 12mm.
Now the flange that bolts the driveshaft to the rearend. But first make a good mark on the flange on the nut and on the pinion gear. That should be inside of the big nut don't know the size of the nut but you could look it up sorry.I'm bein lazy.
But pull your emergency.break to lock the piniongear "your rear end" from spinning.
Put your socket on the nut an make another mark on your socket online with the others you have made already. Now loosen the big flange nut BUT VERY IMPORTANT!!!! COUNT HOW MANY TIMES OR TURNS IT TAKES TO GET THE NUT OFF. THIS.NUMBER IS IMPORTANT. Because when you go to put everything back on an tighten it up. There is a crush sleeve inside that over tightening will damage or basically cause a grinding noise from your rearend. But install the new pinion seal.
An making these marks an counting the turns will let you put the nut an flange back like it was an minimize this problem. Because once you damage the crush sleeve you will have to pull the gears out of the rearend "your second problem"
This is a repair if your not pulling the rear gears. And want to replace a leaky pinion seal?