First here is a link to the Toyota FSM (Factory Service Manual):

http://personal.utulsa.edu/~nathan-buchanan/93fsm/

Do not re-use the wheel bearing seals.

The wheel bearings sound iffy, I would replace.

Pack the bearings and hub according to the FSM.

Are you trying to get the BJ's loose from the spindle?

What is the "proper tool" that you are using? You either need a puller or it can also be done with two big hammers, a pickle fork will work but in my opinion they are a PITA.

As far as the half shaft, the boot may or may not stay on, it should have a clamp holding it on.

Two hammer method of removing TRE's and BJ's.