CSX tracks Newberry,FL and the history of the West Coast sub.?

Lots of questions there that don't really have an answer other than business as usual. 

A lot of the tracks on that map are now abandoned or run by short lines. 

Here is another question, why did CSX abandon the JAX to Savannah route?

I think the answer there is Waycross.

Waycross is a MAJOR hub for CSX. So why maintain all those other north-south routes when nearly everything passes through Waycross?

I disagree with your assertion that JAX is a bottleneck. There is plenty of capacity to handle more trains through JAX. Heck, on Saturday I drove along US-301 from Starke to Ocala and saw zero trains along that route.

The SAL route between JAX and Savannah did have alot of bridges and was only single track.  I see why CSX abandoned it.  The route I am talking about could have been useful as a alternative route from Waycross to Tampa that avoids Jacksonville.  I know Beaver Street can get congested.  I know the Waycross to Tampa/South Florida take the Callahan cutoff that CSX has now double tracked nearly all of it to Baldwin.  The S Line improvements have raised the lines capacity and I guess that makes having an alternative route less important.  I wonder how many through trains at the height of the ACL and later the SCL west coast main saw. I wish there was more pictures and videos of the route during its glory days.