Shoreditch Closure

I would presume it was due to it undergoing more intensive redevelopment - whereas the rest of the line was simply being upgraded, Shoreditch was actually moved.

The original Shoreditch station was in a deep cutting, at about the same level as Whitechapel. The new one is on a viaduct above street level. In order to get the trains from Whitechapel to Shoreditch High Street required that the old cutting be filled in an transformed into a long ramp, and obviously trains couldn't run on the section while it was being done. The track level at Whitechapel station is not being altered, so trains could continue running to this station while the section north of there was being worked on. They started filling in the old cutting between Shoreditch closing and Whitechapel closing.

To simplify think of it like this:
The work on section A will take 3 years.
The work on section B will take 2 years.

In order for both sections to finish at the same time, you need to start section B 1 year after you start section A.