The red/orange stripe is indeed a tribute to the old New Haven railroad... more or less, it seems that the state of Connecticut has adopted the old New Haven look for any commuter rail project it supports. When Shore Line East was started in 1990, they had a couple of F7's painted in the NH scheme, along with a GP40 painted in the FL9 scheme (Athearn would have been PROUD!).
I want to attribute the blue stripe to the MTA... when the MTA began to underwrite commuter trains on the Hudson and Harlem Lines, the ACMU's got a new paint scheme- aluminum with a blue stripe below the windowband- very similar to the paint scheme the R-16's were getting on the Subway... was this MTA's way of making the entire rail fleet uniform? At any rate... blue window bands began appearing on MTA equipment at this time, and later, the FL9's got painted in a blue and yellow scheme (to represent NYS colors). In the late 1970s, the F's got silver and a blue stripe... (and then MN added the red below the blue, most likely a nod to Connecticut) and so on and and so on...
And here are some variations of coach paint over the years:
http://www.tsny.com/otto/mta-1.html
-otto-
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