I'd like to take a look at the full report, but who knows when that will be released. Out of what that Journal article highlighted, I wonder how they'd go about building the Derry-Letterkenny line. As a thought exercise, I'll take a bit of a look at things.
Using RailMapOnline as a reference, in terms of getting to Letterkenny the Lough Swilly route was a bit roundabout, and Graving Dock and the route out of Derry from there is long gone. There doesn't seem to be too much blocking the way out of Foyle Road, but building from Waterside and through Victoria Road might be better for through trains, though the Foyle would need to be crossed somehow. I've also heard rumours about the Derry Road, and the GNR route to Strabane is less obstructed. The approach into Letterkenny is now the N13 and the station itself is now a Penneys. The nearby Donegal approach is less built on, but it still gets blocked nearing the town.
I drew two routes on the map, coloured green: one via Newtowncunningham (population 1,000) and a more direct route. There may be factors I may be missing (i wouldn't know how the Google altitude highlights translate to gradients, for example.)
As for the rest of the things mentioned, seeing Athenry-Claremorris and Waterford-Rosslare come up is good, and the Midelton-Youghal line shouldn't have been turned into a greenway (I'd add Mullingar-Athlone to that too, though I appreciate that Tullamore is a larger town than Moate.) Dublin Airport really should have a proper link to the national railway network, and anything after that would basically devolve into pipe dreams. I dedicated too much space in my own submission to the review to pipe dreams.