DfT must have read the article as they've released an updated version of The Northern Transport Strategy today
https://www.gov.uk/government/uploa...2/northern-transport-strategy-spring-2016.pdf
The Strategy update does not seem to give much more detail than the previous issue. However, Fig.3.3 is a schematic map of "TfN emerging options for the Northern Powerhouse Rail network", with the disclaimer that it is illustrative only and may change.
For Liverpool, the map shows a new line east to join HS2 north of the triangular junction with the Manchester spur. Access to Manchester would be on HS2 via the Airport. There does not seem to be any alternative option.
For Manchester to Leeds and Sheffield, one option is a new line south of the Diggle line, passing southeast of Huddersfield and northwest of Barnsley, and joining the HS2 eastern branch in a delta junction. So rather a long route to Sheffield, shorter to Leeds. The other option is "major upgrades" to both the Diggle and Hope Valley routes; these would include major bypasses and cut-offs, making each route "akin to a new line".
For Leeds to York and Newcastle, "major upgrades" are again being considered, including the ECML section.
For Leeds to Selby and Hull, and Sheffield to Hull, "conventional upgrades" to the existing lines are being considered; these could include sections of four-tracking and grade-separated junctions as well as electrification.
For Sheffield to Meadowhall, there are options for either "conventional upgrades" or a new line.
On the next steps, the document says that:
Outline feasibility work will be completed by Autumn 2016, allowing assessment of the options before
the end of the calendar year.