The seal that leaks causing gear oil migration is inside the transfer case where the output shaft of the trans enters the front 1/2 of the transfer case.
Fel is right on...the bypass hose is a temp fix for a leaking seal. but back to the O.P.'s original question of things to do.
1. rebuild the transfer case. It has to come out with the transmission anyway, might as well rebuild it.
2. get the flywheel surfaced...about $50 at NAPA
3. replace the pilot and throw out bearing. Throw out bearing may come with the clutch kit, not sure about the pilot bearing.
4. Inspect the rubber boot and replace if necessary at the clutch slave where the fork goes in the bell housing,
5. replace the RMS if you are leaking any MOTOR oil at the back of the motor. and it is a good idea to drop the oil pan, remove the crank bearing retainer at the rear and PLACE the RMS...instead of trying to drive it in and tear the inner lip on it. If you do this you'll want to get another oil pan gasket and some Fipg (aka toyota rtv) while your oil pan is off clean the sludge off the bottom and check to make sure the pick screen is clear on the oil pump.