I agree that the Hudson tubes are the biggest concern for the infrastructure of NEC and the big screw-up over funding the third tube (lots of blame to go around everywhere - so no taking sides please) has left that the weakest spot of the Boston to DC segment. I would rate the condition of the trackage at NYC Penn the second major issue with derailments due to deferred maintenance being a continued issue. But where does one truly stop? The Hackensack, Newark, and the Susquehanna River bridges all need to be replaced.
At this point, to properly refurbish one Tube the likely scenarios are a single track or trying to do the rehab work during the night time off-peak hours which could easily lead back to the single track scenario.
As an architect, I can fully appreciate the masterpiece of the original NY Penn. It was McKim, Meade and White's icon in the era of early 20th century neoclassicism down to the plan being based on the Roman baths at Caracalla blended with the still relatively new technology of building with structural steel. However what is often not factored into these projects is the cost of labor has gone up tremendously since it was originally built and we do not have the skilled craftsman like we used too. However with today's 3D technology, by the time a project like this would have a chance to move forward, many of the parts could be built using an electronic model and laser cut and milled bringing some of the cost down.
However, I also know from working in the public sector that due to the length of time these projects take, add twice the scheduled time and budget and you probably have a more realistic project. The new World Trade Center was built during a recession that hugely deflated the construction industry and prices. This recession has not negatively impacted the construction market nearly as much so everything comes at a premium. Final cost will be determined where in the inevitable peak to trough cycles of the construction economy such a project falls.
I have seen photos of the renovations of the post office. Quite a remarkable transformation, but it no Penn Station like people may have remembered. The needs of the modern world would likely dictate that any recreation of the old Penn Station would require similar compromises to the original design.