The rail operator has come under widespread criticism for losing control of the two projects and for its inability to predict when the two key rail arteries would reopen.
The West Coast Main Line was shut from 27-30 December to allow Network Rail and its contractors to carry out a major remodelling of track around Rugby station.
The line was initially scheduled to start running again on New Year's Eve. However, a shortage
of electrification staff led to delays in the engineering works and the track was not reopened until Friday 4 January.
However, Network Rail initially told train operators and the public that the line would reopen just one day late. This lack of transparency over the details has opened them up to widespread criticism.
First Scotrail's managing director, Mary Dickson, said that they would be asking some "hard questions" of Network Rail managers, as the result of having to suspend services between Glasgow and Paisley.
She also claimed that Network Rail was still insisting the work would be completed on time the night before the overrun.
It is understood that the West Coast delays were triggered by a decision to switch engineers from Rugby to London.
This move still did not prevent London Liverpool Street station from reopening a day late, to the anger of Andrew Chivers, managing director of National Express's commuter franchise One.
An email from Chivers to Network Rail chief executive Iain Coucher sent last Tuesday and leaked to the press is clear in its condemnation of the rail operator.
"This is a major failure by Network Rail, first and foremost.
"I was assured that proper scrutiny of the project at Liverpool Street would be undertaken by Network Rail on a regular basis, indeed every eight hours.
The information coming back from this process was not worth reading. As at 0400 (the time of handback) the reports were that the work would be substantially completed and services could operate.
In the end 70 people were required overnight on the 2nd to complete the works that had already been significantly reduced in scope.
"This clearly had nothing to do with Bechtel and everything to do with Bechtel and the way in which the contractor's performance was managed by Network Rail."
At Rugby Network Rail did move to minimise the impact of the decision to switch electrification engineers to London by reprogramming work, with Atkins carrying out signalling work ahead of the electrification works.
But engineers said this week that the shortage of electrification engineers should have been
EPC Global, a recruitment agency specialising in rail, said that electrification engineers were high voltage specialists and were in short supply.
"Electrification engineers are typically hard to find anyway. Maybe they just didn't offer enough money this side of Christmas," said the spokesperson.