Amtrak used to run 90-100 out west all the time, as did the Santa Fe run passenger trains at these speeds long before Amtrak. All you need is a FRA waiver, and most of the route has that already. BNSF will be required by law to install ATC on all of its lines anyway by 2015, unless of course an FRA waiver is issued the other way, for them NOT to do it. That's an unfortunate afterthought of Congress and its knee-jerk reaction to Chattsworth.
So, the 79 MPH "roadblock" thing is just a red herring.
Amtrak's fastest route between Chicago and the wast coast, even as it is now, is the Chief. Yet it isn't coming close to 79 on the existing Chief route though the mountains now, so what's this big deal about lack 'o speed? It's already faster than any alternative.
Where Amtrak runs 90 mph, there is an operational ATS system, per FRA requirements. Cab signalling works, too, but AT&SF never used cab signalling as far as I know. No waiver is involved.
Until about 1948 the FRA didn't really have speed limits and the RRs ran as fast they felt was safe. After 1948, sure AT&SF ran 90 -- they installed ATS so they could exceed 79 mph, per FRA regs. Well, they took out the maintenance intensive (and old) ATS system most places where Amtrak did NOT run after 1971, so they didn't have to maintain it. That includes the Transcon/Belen Cutoff east of Dalies. FRA isn't going to let them run 90 without some kind of ATS.
The PTC (Positive Train Control) system required by 2015 may well fulfill that requirement, but it isn't there yet -- and until then, the speed restriction holding maximum allowed speed to 79 without ATS stands.
And I wasn't actually arguing about using the Transcon/Belen Cutoff or the time required. Even though ATS remains on much of the line through Kansas, BNSF and Amtrak agreed to drop the maximum speed to 79 there anyway. Most of the 90 mph running is west of Dalies, NM, with some in Missouri, neither part of the potential re-route. What I was arguing was the assertion that Amtrak could run 90 without the FRA required signalling infrastructure to run that speed. They can't and don't.
BTW, TVRM60 - CTC is "Centralized Traffic Control" -- dispatcher controlled signals and switches. Many, many mainlines have CTC. Having CTC still limits you to 79 mph without some kind of automatic train stop or cab signalling in addition to CTC.