A couple of things about my position that I need to clarify.
First off, I do NOT think it's a good idea to break up the NEC. That's stupid. That's the way it was built, true, split between the PRR and NYNH&H, with the NH's tracks further split between electrified and non-electrified sections. After literally a century of talking about it, finally that problem got fixed; the last thing we need is to artificially reinstate it.
Splitting off the Empire routes makes more sense, because AFAIK they're operationally totally different. I mean, they have to use completely different equipment because the electrification is third-rail or absent.
It might make logical sense to consider the Keystone corridor as part of the NEC, again because it can use more or less the same overhead-electric equipment. I dunno if that's necessary or not, but it's reasonable.
My split-things-up argument applies only to separating the NEC and its direct tributaries, from everything else. Ideally, I'd split up the everything-else too, such as the California services (well, maybe the whole Pacific Coast). The idea would be to isolate the areas of the network that might be self-sustaining, so they won't collapse with the weight of the no-hoper routes.
As far as the infrastructure goes, I am fundamentally opposed to government funding of these sorts of things, precisely because neither the Feds nor the states can be relied upon to come up with the dough on the CONSISTENT, PREDICTABLE, REGULAR basis required for rail operations. With a highway, you can extend it one exit at a time if need be, and it's still useful; not nearly so true with rail service. And the capital operating costs are much greater. If there needs to be a government subsidy, and in some places I can see arguments for one, I'd say it should come only in one of two ways:
1. Eliminate property taxes on railroad property and equipment. Once that's done, you don't have to fight through the budget process every year, just once in a while when some pol casts his beady eye on the tracks.
2. Strict funding on a commission basis, that is, a payment per passenger-mile travelled. You could write this as a multi-year contract which would be legally enforceable. The military does this regularly, for the express reason of making the contracts difficult to cancel; it's good business because it eliminates (well, reduces) some of the budgetary risk for the companies involved, that they normally have to add to the costs when doing business with the government.
Concerning private enterprise, why are we so allergic to it? Private enterprise has always been shown to be both more efficient and provide better service than government-run services. Where private enterprise fails, it is either because there is not sufficient demand for the services, or because the government has been incompetent in setting up the regulatory environment or the incentives. "Give me perverse incentives, and do not be surprised if I act perversely." Hence my suggestion of the simple, straightforward passenger-mile subsidy.
I don't have a position about separating the roadbed from the trains. In theory it sounds like it ought to work, but AFAIK it's never actually worked in the real world. Now, maybe that's because the various governments involved botched things, Britain certainly did. Maybe it's because railways are inherently too complex for the contracts involved to be sensibly written, so as to set up proper incentives and costs. I just don't know. I agree, it seems fishy in the case of the NEC.
As far as duplicating the administrative activities, you're probably right that that's what would happen, but it needn't be that way. In fact, a more logical method would be to combine Amtrak/NEC with the various state operators (NJT, MARC, MBTA, ConnDOT, MetroNorth, and whatever RI and DE chip in) into one operating group. This would be more efficient in many ways, not least buying equipment in bulk. What's wrong with standardizing on the HHP-8, one electric MU, one single-level traincar with alternative commuter and long-haul interiors, one commuter bilevel, the Genesis (OK, with some having the third-rail capability), and of course the Acela Express. One need only look at Southwest to see the advantage of reducing the number of equipment types, and buying new equipment identical and in bulk.