So with that info in mind, here's the scenario:
Double track the West Shore between Fairport and Chili.
Build an Amshack somewhere near MCC or Marketplace Mall
re-lay a couple tracks at Genesee Junction Yard.
All Kodak traffic could be handled by R&S via Genesee Junction
Rochester Lumber has a plant adjacent to ONCT - put in a siding
Keep a short stretch of track to serve Contisano in Fairport
Abandon and sell off the main from Fairport to Chili Jct
The two or three customers who would be totally lost would be more than made up for, by the savings in taxes and sale of real estate in downtown Rochester. The city would probably LOVE to get rid of the railroad bridge just above High Falls, and CSX would probably benefit from not traveling through the middle of the city - i.e. vandalism, lawsuits when kids hop rides, theft from stopped trains. CSX also gets rid of the close clearance near the Depot, not to mention the entire Charlotte branch. Depending on how persuasive the mass transit advocates are, the city might take over the Charlotte Branch as access for the teeming masses flocking to and from the Fast Ferry
About the only negative would be opposition from the NIMBYs in Pittsford - if CSX were able to bridge over or under Monroe Avenue and a couple other crossings, it would work. Too bad Scottsville Road has just been reconfigured, that would be a problem area when working at Genesee Junction.