I like your idea up until Victoria but,after that, I would like the line to service Charing Cross
Err, why? If you go to Charing Cross instead of Waterloo, you lose the connection with the entire SWR service from Waterloo, and gain nothing in connectivity, since every train or tube at Charing Cross that people might want to connect with also goes to Waterloo (and if you want interchange with the District and Circle at Embankment, Altnabreac's proposal already gives that at Victoria). You do gain convenience for anyone whose final destination is within walking distance of Charing Cross, but it looks to me like you've lost far more than that. (Although maybe it's more build-able at Charing Cross with fewer conflicting underground lines?)
, a station on Walbrook equidistant to Cannon Street and Bank,
Not sure if that's physically possible around existing lines, but you do realize, that risks running the new line right through where the
new escalators etc. are being built at Bank? It would basically make it part of Bank station.
then Fenchurch Street underground to take LTS stopper metro services out to Southend Central and Pitsea via Rainham and Grays, the tunnel portal could be where Tower Gateway is today and a new Tower Hill DLR created,directly interchanging with the Tube.
If you are going to close Tower Gateway (arguably not a bad thing), wouldn't it be cheaper, simpler, and more useful to most people to just run the displaced DLR trains to Bank (assuming there's capacity there? But you're not talking that many trains anyway) You can still connect with the District and Circle lines at Monument.
Fenchurch St would then just take fasts to Southend Central and Shoeburyness and it could take some fasts off the GEML via the Bow Curve to allow for a service increase on the WAML or possibly the GEML itself.
Running services via the Bow curve would cause huge capacity issues due to the conflicting moves, unless you built grade separated junctions at both ends of the curve.
The LTSR could be upgraded to 125mph for the fasts.
Uh? That's a two-track railway that already runs a fairly intensive stopping metro service. There's no way you could run 125mph trains on it without them quickly catching up with the stoppers, so you'd need to 4-track somewhere. Besides, 125mph running is usually only worth it for longer distances. Southend is only 40 miles from Fenchurch Street. If you (optimistically) got even 30 miles of that at 125mph, and ran non-stop Southend-Fenchurch Street, you'd only save 3 minutes compared to non-stop 100 mph running. And to do that, you'd have the fasts missing out a lot of stations that are just as busy (or even busier) than Southend. Plus you'd probably have years of intense disruption along the line to do the upgrades. Realistically, you'd probably want to stop even hypothetical new fast trains at least at West Ham and Basildon, and that would really make 125mph running not worth it. It would be great if a new Crossrail link allowed more trains onto that line, but you'd be far better running them as semi-fasts.
The LO Romford to Upminister service could be extended back to Tilbury as it used to go.
Meaning it would have to cross the LTSR at Upminster requiring new grade-separated junctions if you don't want to kill capacity. Would there be enough demand for through journeys to Romford to justify that expense?
Marylebone could then accommodate more fast services from Birmingham and various points on the rest of the Chiltern Main Line.
That would be great, but probably only possible with capacity upgrades along the Chiltern line out of Marylebone.
Potentially,if money is no object, there could be a branch continuing from Fenchurch St underground under the Thames to Bermondsey tube,South Bermondsey for the Den, New Cross(interchange with the Overground and the Goldsmiths campus),Lewisham underground station(potentially future proofed for a Bakerloo line extension), then a tunnel portal at Hither Green as another user suggested and all stops to Orpington and Sevenoaks.
That bit would be a good idea.