Since we've got the crayons out, how about resignalling the York - Northallerton line to be paired by use (fast lines to the east). The 3 track bridge at Skelton Jn would complicate it, but the platforms at Thirsk are in the right place at least, and it would match the 4 tracks south of York.My pick for grade seperation would be Skelton Jct above York, if a flyover was constructed running parralel to the outer ring road then the Harrogate line could connect with the Scarborough line and avoid the need for services to and from Harrogate to use the ECML.
I don't know when ETCS is due up there, but that would be the ideal opportunity to start from a cleanish sheet of paper.