I think the only easy way to add some split levels is this.
Remove the yellow track and make oth main lines rise and fall, the highest point being above the dock area.
Here's a picture then the explanation...
Reattaching the green line to the main line at the TMD somehow, thus negating the need for the yellow track.
Keep this track/station/TMD all on one level.
Move the point to the docks line (is this what you mean by your branch line?) circled in black to this new upper place, so you still have the functionality of getting onto the docks/branch line.
All the blue twin track in the green boxes can now be raised. The incline starting after that new point position on the right, raising up then going behind the docks at height then declining before reaching the points on the left hand side.
It's the easiet soloution I could think of for split levels but may not reach 4 inches above the docks/branch line.
Hope it helps.
Thanks
End2end
EDIT: I just thought, if the blue track
was raised behind the docks, arches would make some great oppertunities to use them as warehouses and a fake road entry/exit!
