I've started using aluminum tape to seal the breather port (on top the trans) while working. It not only sticks well, but holds its shape, so is less likely to pull off. Clean the port by hand with a degreaser or brake clean first to get a good seal.
I usually take the transmission to a coin operated car wash first to get a good first pass. Wear nasty clothes, because it'll spray back at you most of the time. Then I use purple degreaser and brushes, picks, and scrapers. In my experience, no matter what, you're going to spend some time just manually cleaning it.
As far as replacing the seals, you need a seal puller tool (the hooked kind) to get most of them out.
Input Shaft Seal-Remove the throwout fork with an allen wrench.
-Remove the guide tube using a 10mm socket wrench.
-Use your seal puller to pry the old seal out.
-Install the new seal with a piece of pipe, or a special tool
like this one. There is a slight lip inside the bore. I stop when the seal is flush with that lip.
-Bolt the guide tube back into place.
-Lubricate the guide tube.
-Reinstall the throwout bearing/fork.
Output Shaft Seals-Turn the transmission on it's side, so the gear oil won't run out (you plugged the vent port, right?).
-Thread two 8mm x 1.25 bolts into the output flange and place a screwdriver between them to pry against.
-Remove the bolt in the center and slide the output shaft out. Be careful not to let crap fall into the innards.
-Pry out the seal with your puller.
-Install the new seal using a large flat piece of steel and a hammer. Drive the seal in straight. If it gets very far cockeyed then it can deform and leak.
-Reinstall the output flange and bolt.
-Torque bolt to 25-29 ft. lbs.
-Do the other side.
Shift Selector Seals-The shift selector has a seal and an o-ring.
-The selector should be in neutral.
-Remove the two nuts with a 13mm wrench.
-Pull the whole assembly away from the body. It slides out in a very particular way. So don't fight it. Just keep trying.
-Take note of the orientation of the ends and where the plastic washers are.
-You now need to remove the roll pin from the selector end of the shaft (the one inside the transmission). Simply drive the roll pin out with an appropriate drift/punch. Don't remove the roll pin from the ball end.
-Pull the shaft out and pry the seal out with whatever works (seal puller, screwdriver, hook-end pick). This one is hard to get.
-Install the new shaft seal.
-Slide the shaft back into place with everything back the way it was, and reinstall the selector end and the roll pin.
-Remove the o-ring and replace it with the new one.
-Install the completed console with no gasket. Use some light sealant if your worried.
-Reinstall the nuts.
Speedo Drive O-Ring-Remove the special bolt at the back of the transmission using a 13mm socket.
-Slide the whole speedo drive assembly out of the nose cone. This can be challenging.
-Remove the old o-ring and install the new one.
-Replace the internal seal as well if you're inclined. Just remove the angle drive, slide the shaft out and then remove the old one and put in the new one.
-Slide the drive assembly back into the transmission nose cone, being careful to align the small hole/divot with the threaded boss.
-Look past the threads to confirm the small hole/divot is centered and reinstall the special bolt. Only just tight enough. Too much torque will strip the threads. I've seen it plenty of times.
Notes-You might have a leak around the special ball pivot that the clutch fork rides on. You can remove it with a deep 13mm socket and use a sealant on the threads.
-There is a white plastic bushing in the clutch fork ball pivot that should be replaced.
-Make sure to lubricate the throwout bearing guide tube, otherwise the bearing may not slide smoothly on the guide or may even get stuck in one position.
-Don't forget to remove the aluminum tape from the vent port before reinstallation. A plugged vent is a sure way to get leaks.
-The muffler hanger will sometimes rub on the transmission nose cone and wear it away. I've seen a transmission that had worn enough to cause a leak.
-Check the rear mounts for cracking.