Is it possible to get the boot that goes around the shift lever? There are 3 boots in total, this is the inner most boot. My center section around the shift lever is torn away allowing dust and dirt to get onto the ball that allows the lever to pivot. I feel like I should replace this while I have it open for a clutch job. Should I not worry about it?

 

That part seems to be obsolete, non-existent. Probably you'll have to buy a new shift tower, but beware of those cheap chinese made, apparently they have some fitment issues. Or, try looking one from the junk yard.

 

Is item #4 the entire tower or is it just for the lever?

 

Probably it's entire tower. Everywhere I looked, listed the whole shifter. I did find a picture that had a that boot numbered, but it was not listed, only the tower.