See my earlier post regarding depot access.
I have, you haven't demonstrated anything other than talking about 'slueing' buildings. Most important is the road and car park in, which will have your new chord slap bang through the middle of it, but about 1.5m below the current ground level. So no level crossing, but also not a lot of room for a bridge.
Please can you tell me what work you had done regarding 'standage and gradients'
Some very rudimentary calculations using google maps's 'measure distance' feature, laser scan /3d model of the area, and knowledge that the minimum height above the railhead is c.4m, + tunnel lining and earth above that to work out the vertical separation. It looks to be from some rather basic reckoning at least a 6m vertical separation between the tracks, and a maximum distance between the two lines of 400m or so. Evidently, that's steeper than the 1:100 recommended gradient for freight. The margin of error is sufficient that even if I'm pessimistic the improvement wouldn't be sufficient for a freight train timed at up to 2400 tonne trailing load.
Do you think keeping long and heavy freight trains on the main route into and out of Liverpool is a good idea ?
I think it's a much better idea than trying to run a freight on a metro route. The 4-track section at Huyton and Roby provides a regulating section and you have 2 different routes to reach Wigan NW, one of which has some very underutilised Slow/Goods lines from Golborne Jn. You'd have to wait for a bit at Wigan Station Junction or that area for a slot on the 2-track section through to Euxton Junction but there's space, and a decent amount of it.
Merseyrail is to all intents and purposes a heavy metro along the lines of the London Underground and keeping it as self-contained as possible is the best course of action for the people who use it.