CMC, IMO, the s55 or any bus should not go into Perth Amboy downtown or to the rail station, it should stop along Route 35, at the QuickCheck (in Perth Amboy), stop at Main Street (Woodbridge) (5 minute walk to Woodbrige NJCL station) then go to Woodbridge Center (major shopping and office parks) and then end at Metropark (NEC, Amtrak, officeparks). Cheesequake should not be considered.
Secondly, not many folks from NJ are going to take transportation to the Staten Island ferry. Off-peak and weekend service on the NEC and NJCL isn't that bad. Bus service on the 116 which duplicates the NJCL is pretty consistent. Personally, with the availability of express buses, I wont consider the SIRT/SI Ferry unless it is very late at night.
Also, there is no way for a hypothetical North Shore SIR to connect with the NEC/NJCL lines. First there would have to be some massive eminent domain seizures in Elizabeth and the rail bridge going over the AR Kill connects with freight railroads, none to my knowledge connects with the Amtrak-owned lines which NJ Transit use for NEC and NJCL service, with a possible exception that there could a cross over in Kearny then onto Newark (essentially they would have to go east and then back west and east again at Newark Penn. Additionally, unless the MTA runs DMU, Diesel multiple unit rolling stock (the equipment used on River Line) OR they purchase or use hybrid diesel/electric trains that is compatible with the Amtrak/NJT/freight systems then along with the resolution of the logistical issues above then we could connect to the North Shore SIR system.