Can anyone give me some advice on removing the S-tube on a Transcrete Line Pump? I have all the bolts removed but noticed a large square key on front shaft. Does this need to be removed before the S-tube? 

Stick a length of 4x4 down the end of the S-tube and jerk up and down, left and right to remove the S-tube from the shaft.

Naturally, you have already removed the outlet flange aand outlet seal housing!!

When you replace the S-tube make sure it is fitting square to the shaft face. apply anti-sieze to the 4 bolts.

Remove hard slurry from the inside bore of the seal housing, apply grease to inside the housing and also the seal. 

Yes, removed outer housing and seal. I'm thinking this entire rear housing needs to clean. There was no grease getting in there. 

Does the rear housing come out as one unit like a boom pump would? 

The outlet flange holds the seal housing in place. The outlet seal housing is one piece with the seal inside.

Seal is removable, just drop face down on concrete floor and the seal moves out.

Pack with grease, graphite type best type.