New Main Panel & Sub-Panel - Hooking up Ground / Netural - Connecting to Plumbing / Ground Bar
I'm fine with the idea of a main panel with only 2 things in it feeding a sub-panel with everything in it.

Question #1 - I'd rethink putting a service panel outdoors at all. Weather is rough on panels, even if they claim to be outdoor rated.  I'm a little nervous about a 100A breaker supplied from the normal bus bars, but if the manufacturer stands behind it, okay.  The 100A wires are going to be a mother to wrestle onto that 100A breaker.  Are you quite sure the power company has provisioned you 125A service?  100A is more common.  

Question #1 (the second):  You're gonna want more slots than 24, since this box powers pretty much your whole house.  Nobody ever installed an addition and went "Gosh, that job was sure made harder and more expensive by having too many slots in the panel".  It's a false economy, especially since bigger boxes are often bundled with more breakers.  Your house may be ok now, but do a kitchen remodel and lookout! 

Question #2 (the second):  Don't bond your grounds to random plumbing that happens to be going by.  It's not code, and someday you might have a plumbing problem and the plumber replaces a downstream chunk of it with PVC.  Whoops. Also, they've been upgrading customers to PLASTIC water meters. Double whoops.  Bond properly and to code. 

Question #3 (the third): Bond ground and neutral only in the (singular) main panel. As such, you need 4 wires between main and subpanel. 

Just for your edification, it's only a sub-panel if it's fed from a main panel. If it's fed directly from a transformer, it's a main panel.