Some of this looks a bit far fetched to me, particularly the reintroduction of freight into Birkenhead Docks (to be known as Wirral Waters) via Bidston.
Presumably some gauge enhancement would be needed for further development of container traffic to Liverpool?
As far as I know the Bootle Branch which links the Liverpool dock estate with the Chat Moss is already cleared for container traffic. As far as Birkenhead Docks are concerned, plans have been announced to develop the area as Wirral Waters.
http://www.wirralwaters.co.uk/
From a freight point of view the present dock facilities are not suitable for modern containership operations some parts could remain active serving bulk cargoes, albeit in relatively small ships and distribution. Personally I don't think rail freight will return to the Birkenhead dock system but in view of the proposed residential and commercial facilities might allow some form of passenger service being provided perhaps using a light rail system.
Ellesmere Port and Port Salford are both being developed by Peel as freight centres on the Manchester Ship Canal. They already operate a 350 TEU vessel up the canal from Seaforth to Irlam two or three times a week that makes inducement calls at Ellesmere Port. The plan is develop both sites as freight villages with facilities for stuffing and devanning containers, as well as distribution. Whether the types or volumes of cargo handled will be sufficient to justify a rail connection remains to be seen, although Ellesmere Port will retain the capability to handle bulk cargos but like all locations on the canal is limited to the size of the ship that can navigate the Canal.
Perhaps it's also worth mentioning at this point that Peel Logistics have purchased the former Sonae site at Kirkby which is adjacent to the Potter facility which is rail linked to the Kirkby Wigan line. The Peel scheme is being marketed as Knowsley 700
http://peellogistics.co.uk/sites/knowsley-700/#.VFviQc-285s
The Kirkby to Wigan line is due to be cleared for container traffic in the near future as Potter have secured a contract to move containers from the site to the North East. At the moment there is no direct connection between the Bootle Branch and the Kirkby Wigan Line but the former does pass under latter at Kirkdale. It may be possible to in the longer term to construct a connection on the south side of station running parallel to the existing Kirkby line restoring the line to four tracks as the tunnels all remain in place.
Unlike Felixstowe, London Gateway and Southampton, the Port of Liverpool handles both bulk and container traffic although currently there are no intermodal trains using the Seaforth facility for reasons which have been explained in other thread. The opening of Liverpool2 will change this because of the wider range of vessels that will call at the port and the growing shortage of truck drivers remaining in the industry. This is fast becoming a major problem because more and more 18000 teu vessels are being introduced into global trade. Southampton is already struggling to cope with them with delays of up to five or six days being commonly quoted to deliver a laden 40ft container to the North of England due to the lack of train space and road haulage capacity. As these delays build up the stacks in the terminal also become full making it difficult for the port to load and discharge ships on schedule resulting in vessels being delayed and knock on delays in following ports and huge additional costs for the shipowner. Southampton's largest customer, the G6 alliance which is the join service of Hapag Lloyd, OOCL, NYK, APL, Hyundai and MOL currently only operate a small number of 10000 to 13000 teu vessels, but rumours are that they will be order 18000 + vessels in the near future although they are unlikely to be delivered before 2017. By the time Liverpool2 opens there will be a strong demand in the North of England to find alternatives to these problems so it is possible that Liverpool2 could gain some healthy support from some global carriers.