I don't think the actual count is 100 tracks, but the numbering goes over 100. A lot are OOS because they're passageways, etc. DRN should know.
Ok - now, isn't there also a super secret power station lower level of GCT that we all know about but aren't supposed to know about and nobody really knows about it anyway?
I'm wondering if that is really where the MTA wants to stick the LIRR terminal, in which case , it would actually make sense. But the MTA is really tight about details about anything...
The high line is effectively a gonner. There's quite a few legal issues surrounding use of it for ANYTHING, letalone a rail line. Among other things, Conrail never abandoned it (they thought they did, though), yet the line got built over. Because Conrail never contested this construction, and it was in place a long time, I believe a lot of it actually is legal (effectively, Conrail never protected their assets, thus they gave them up in a sense. This is why companies go bonkers over trademark issues - they can lose their trademark if it is not enforced).
And, it's falling apart.
As for LIRR to downtown via 2nd ave? They're going to have to tunnel anyway, and if it's cut and cover, the extra cost of another 2 tracks might not be much at all. Even if it's a 40mph line (and if it's straight, there's really no reason it can't be 60 or even 80), the time to get from 42nd street to Wall Street by train wouldn't be much, and it'd be faster than getting off at GCT and taking a subway. I bet you could relieve a LOT of traffic on the subway, which would mean also that local traffic would be better served by the east side lines - ever try using the east side IRT durring rush hour?
Besides, it'd be funky to see LIRR trains running on the 'express' tracks of a subway line
BTW, I believe the MTA did in fact consider mixed operations when the M-1s were ordered, I recall reading that they were considering a plan where the LIRR would go to Wall Street via the A/C/E trackage.