if the oil is really old and nasty, then i like to run both units on ATF for a few miles. the detergents and additives in the ATF will help clean up any sludge or buildup that has accumulated. drain it after you have run it for a few miles and then replace with gear oil.
whils the units are out, it's not a horrible idea to replace the transfer case input seal along with the front and rear output seals as well. you'll need the adapter gasket between the trans and t-case to complete the job.
the seals and gaskets can be bought at the local toyota dealer for a reasonable price.
i alos like to take a good look at the front bearing retainer on the transmission, namely where the throw-out bearing rides. clean the area well, polish with some emery cloth if need be. then apply a little new grease and the clutch will work smoothly. make sure to clean and properly lubricate the clutch fork at the pivot and the slave cylinder push rod engagement point as well. i like to use anti-seize in these two spots.