Phase 1: Quadruplicate from around Officer/Beaconsfield to Clayton on the surface in the spot where it'll be relatively easy/cheap. Vlines shift on to new track around Officer/Beaconsfield and run all the way to Dandenong by themselves, Pakenham shifts on to the new track pair before/at/around Dandenong. Cranbourne line becomes the main / existing pair. All Pakenhams SAS Pak-Dandenong, then express to Clayton, then SAS with Cranbourne trains to Caulfield then express to Anzac/into the MM tunnel. All Cranbournes SAS via Dandenong to the Caulfield then express to Anzac/MM Tunnel stations. All Vlines express Pak-Dandenong-Clayton. All Vline trains terminate at Clayton while phase 2 is under construction.
Phase 2: Quadruplicate (surface) to between Huntingdale/Oakleigh then a tunnel to Chadstone, Caulfield and then straight to Southern Cross which then joins the RRL train pair which Geelong / Traralgon services currently run into. Pakenhams SAS Pakenham to Dandenong, express to Clayton, Chadstone, Caulfield, Southern Cross, Footscray, Sunshine then head off to the airport / Sunbury. La Trobe Valley Vlines can through-route to one of the western lines from Sunshine (it'd be great if it were Bendigo - especially if MARL becomes a Bendigo line deviation just as much as a way of getting rail to the airport).
Phase 1 should be timed to open at the same time as SRL phase 1 (which will link Clayton to other destinations) opens. From Clayton, the SAS to Caulfield and then express to Anzac journey on a metro train will be around ~25min (based on 20 min journey Clayton to Sy using existing stopping pattern) which is a much better (temporary!) scenario for changing trains for Vline / La Trobe Valley passengers.
After Phase 2, LV Vlines could operate on two simplified patterns:
1. [From Ballarat/Bendigo/Geelong], SX, Caulfield, Chadstone, Clayton, Dandenong, Pakenham then SAS to Warragul & vv.
2. [From Ballarat/Bendigo/Geelong], SX, Caulfield, Chadstone, Clayton, Dandenong, Pakenham, express to Warragul then SAS to Traralgon/Bairnsdale.
3-4 TPH for Vlines and 10 + for Pakenham will fit snugly in a track pair, especially as they're doing the same stopping pattern between the city & Dandenong.
Pakenham/Cranbourne likewise simplified:
1. From Airport/Wyndham Vale, SX, Caulfield, Chadstone, Clayton, Dandenong, SAS to Pakenham.
2. Fram Melton/Sunbury/West Footscray, Sunshine, SAS to Footscray, all MM tunnel stations, Caulfield, SAS to Cranbourne via Dandenong or terminate at Dandenong or Westall if needed.