I don't know what the specifics of NJT's federal monies agreement is, but in Chicago, we have two similar examples:
1. CTA 2200 cars were financed by federal money related to the construction of interstate highways here, because the interstate had rapid transit down the median. When the line that goes down the median of the Eisenhower Expressway was subdivided, and one subdivision (pink line) didn't go down any medians anymore, they had to ensure the 2200s weren't operated on the pink line because the 2200s were specifically funded for interstate-related rapid transit.
2. Metra replaced their 70s-vintage 600s with the 400s. Two of the 600s had been rebuilt in the 90s with federal money so they couldn't be sold to Helm or NRE along with the rest of the fleet. Funny thing is, after being laid up and stacks capped, they returned to service after 5+ years due to a traffic crush. Everybody thought they were going to serve their gov't-mandated time in layup and then be razor blades just like the ALP44s, but they didn't, they came back. 614 even blew a generator and was returned to service a few weeks later. The Chicago foamers love 'em so much that there's a tracking thread in our forum. Me? I can't get all that excited about an SD40 with cowling...
The new Acela: It's not Aveliable.