One of the findings of Northern Hub was just that: you need to do something with Ordsall Lane Junction to get it all to work. Sadly grade separation of this junction is costly and not without a few issues, but I'm sure the GRIP3 designers will sort it all out. What happens to Salford Central remains the subject of debate, shall it have 2, 4 or even six platforms?
Elsewhere (thread-wise) I noticed comments about Vic-Staly electrification; this makes sense as the more Liverpool-Manchester electrics you don't turn back at Manchester (Picc or Vic) the more capacity at Picc/ Vic improves. Ferpection would be running all Liverpool - Manchester electrics through to Leeds. You'd only electrify Guide Bridge - Stalybridge as a diversionary route, because it's the slower way round to Stalybridge.