I am 99% sure that my pinion seal is leaking, and that I also need a new pinion bearing (and possibly some other differential work.) The most obvious thing that leads me to believe this is the leak where the axle shaft comes into the differential (picture below). Additionally, my car sometimes thumps when I get on and off the gas, and it makes a whine in overdrive at around 30MPH. I would assume that the whine is transmission related if it didn't sometimes persist after letting off the gas. What exactly do I need in order to replace the pinion bearing and seal? I am a little intimidated by the process, but I want to do it myself.

If it's leaking and been leaking for a while it might be low on fluid. Could be the cause of the whining noise you hear.

that definitely looks like the seal is leaking.
replacing the seal itself is pretty basic but requires getting the car in the air far enough to work comfortably and SAFELY. there are some youtube videos of garages doing it on a lift if you want to familiarize yourself with it before hand.
I've done it twice on my 01 and once on my 03.
the basic steps are:

1 mark a line on the driveshaft, pinon flange and pinion nut so that you can put them back inline

2 remove the 4 bolts holding the driveshaft to the pinon flange and drop the back of the driveshaft...then slide it out of the transmission and set out of the way

3 if you have a dial gauge torque wrench, put it on the center nut and measure the preload on the bearing by turning the gear...this will turn the wheels..they need to be off the ground to do this. the object is not to tighten or loosen the nut; just see how much force it takes to turn things. if you don't have this equipment, mark the outside of your socket with an alignment mark that matches the mark you made on the flange and count the number of turns it takes to completely remove the nut...then you can put it back on with the same number of turns.

4 use a 3 jaw puller or flange puller (free Azone lone a tool) to remove the flange from the splined pinion shaft (note, if you didn't drain the rear end first...you're going to get wet at this point)

5 remove the old seal

6 install in reverse order, the flange can be driven on with the nut as long as you count the number of turns while you do it or back the nut off and start again while counting. do not back the nut off once you've reached the final number of turns...better to be a little tight at that point

there are other methods and added things that should or can be done...like replacing the crush sleeve, but for the DIYer this works fine IMO

also, this is a great time to replace u-joints since you already have the driveshaft out, and vibration from bad u-joints will kill a pinion seal

Thanks for this. I'm already plenty comfortable lifting the car up far enough to work; I do it all the time. It's just that this is my first time working on any part of a car with gears, which is probably why it's a little bit intimidating.

Old thread, but I wanted to post my experience with replacing the pinion seal..

I ended up taking mine to a shop down the street from where I live and got them to do it, I don't have a lift, a 12 point 12mm socket or a puller.

The mechanic did a few things I thought were a bit cringe worthy, he used a impact and took the 12mm bolts off, tied the driveshaft up out of the way, market the nut/flange/pinion with a chisel then used the the impact and took the nut off, took a ball peen hammer and knocked the flange off, ripped the old seal out with a screwdriver, cleaned and lightly sanded where the seal seats itself, then sprayed it with brake clean, rubbed some kind of sealer around the new seal, beat it in the a piece of pipe with his ball peen hammer. Put the flange back on, hit it with the hammer to get it partially on, then put the nut on the pinion and used the impact to snug it down, frequently checking the play by turning it.

I hesitantly mentioned about the play and how most people mark the nut/pinion and count the number of turns when they take it off so they know exactly where it was for when they put it back on. He said that takes too much time and he could tell that it was where its suppose to be by the amount of play when turning it by hand. Then he bolted up the drive shaft wth the impact and that was it. I noticed he didn't use loctite on the 12mm bolts or the pinion nut. The job took 45min and the seal was $20. Needless to say, from watching all that I could of easily done it myself.

The car drives fine, and feels right. But if you over torque that nut, its going to be a lot harder on the bearings and you'll be back in there replacing stuff in no time.