Jerry:
I had an 83 Toy 4x4 and researched this issue extensively. From most sources, the answer was the input shaft bearing. Here is something that was posted on a Toyota site. Hope it helps.
David
Here's a test, Put the Trans in neutral, start the truck clutch in, then let the clutch out,and back in. Is there any bearing type noise humming of a worn or bad bearing? In this mode only the input and counter or cluster gears are turning,the output shaft is not. So if it s really noisy it may be the input shaft bearing,common, or the cluster shaft bearings,also common,but not as much as input shaft. With the fact you stated before about no noises in 4th gear,which is direct drive,leads me to believe that the input or counter gear bearings are bad. Also check your center support bearing ,if equipped,and the front u-joint...yup I have had them make the same weird noises. If the input shaft is worn and sloppy it may give you the hard to shift problem as well, beware if this continues you can count on spending more money than just bearings, stop now and tear it apart and check it before it eats up the gears. If the clutch is worn the diaphragm will become flat there by making the through out have to go farther to disengage the clutch disc, this is very common as they wear down. SO there you go ,step one
1# check for noise in neutral.
2# if no noise proceed to checking u-joints and support bearing first.
3# if they check ok then head into the Trans, but first jack up rear wheels and put into gear and shift slowly through the gears, then listen for noises ,take notes. Get a Toyota repair manual if you can and look at the Trans part, read and be careful to follow any and all instructions. Careful disassembly can prevent the unnecessary cost of parts that were not broken before you started...;) Hope this helps