How close does the boot have to be to the transmission on the driver side axle I got it really close and it looks flushed but not quite does it have to be all the way up against the transmission to be flushed are locked in?

 

So axle didn't click in. If not make sure it does it will fall out while driving

 

There's an intermediate shaft, right? Are you talking about removing the outboard axle-shaft or removing the intermediate shaft?

The intermediate shaft is held in by the bracket on the engine block - it doesn't have a snap ring like the other drive axles.

For the outboard axle shafts, this shows how you get in there with a pry bar, so hopefully it shows you how much space is supposed to be there.