I don't think the above is quite correct. While it will be some time before it is known exactly, I believe that there is a push to differentiate services between TPE (major cities), Northern Connect (major cities and medium sized towns) and Northern (all stops).
So two St Helens stops wouldn't seem right for the TPE, and my bet would be on Newton Le Willows for both of the TPEs as a midway stop between Liverpool and Manchester.
The stopper service from Liverpool to Manchester Victoria I believe will remain but be joined to the existing service from Bradford to Manchester Victoria, to simply create a through route.
The TPE that currently runs via Warrington is to be replaced by a Northern Connect service, which will provide the same level of service but as said above run to Manchester Airport or possibly Leeds.
The new Northern Connect service from Chester will run to Leeds, and will likely only stop at Runcorn East and Warrington Bank Quay.
The other services I think will remain as they are today.
From December 2017- so when Scarborough trains switch to Chat Moss, TPE are required to provide 1tph at each of St Helens Junction and Newton-le-Willows.
By December 2019 (some probably come in earlier, but I'm not sure which or when)
Liverpool-Bradford is to be a Northern Connect service (and diesel), so one would assume it to not be a stopper. It is required to call at Huyton.
The Northern Connect Warrington Central service is shown on the map on the website as running to the Airport, and in any case can't get to Leeds as Northern aren't going to operate anything from Manchester-Leeds via Huddersfield.
Chester-Leeds is only required to call at Warrington off-peak, at peak times nearly all stations. A second Northern service to Manchester must be provided at Earlestown and Newton-le-Willows, so either the Bradford or Chester services must stop there.
Northern are required to provide 1 tph between Liverpool and Manchester Airport calling at Newton-le-Willows. It has been assumed that this is the stopper, as a) it's electric, b) it's not Northern Connect, c) it was in the ITT.