I think this must have happened in stages.
From when I started using them circa 1980 the primary Sheffield-York route for Cross Country was from Wath Road Junction (Swinton) via Cudworth to Goose Hill Junction (Normanton), then on via Castleford to York. I think those running via Leeds must have come off at Altofts Jn - the curve from Moorthorpe to South Kirby is shown as freight only in the 1980 Baker.
With the completion of the curve from Swinton towards Mexborough in about 1987 the main Cross Country route became via Doncaster, with Leeds trains running via Moorthorpe. Wath Road Junction to Cudworth North was closed completely and Cudworth North to Goose Hill plus Castleford to Burton Salmon closed to passengers. The Sheffield-Leeds local service also started to run via Moorthorpe at some point, reducing the need for Sheffield-York trains since Leeds would have been a more attractive destination at the southern end of the route.
I don't recall Cross Country running via Baghill during the 80s although I imagine it would have been a diversionary route.
There's a very complicated history here. The S&K was built by the Midland and North Eastern companies to provide a fast direct connection between their two systems avoiding the delays on the old main lines, especially in the Normanton area. Leeds and Bradfor trains continued to run via Normanton; York and Newcastle ones moved to the new route. The MS&L muscled in on things (as did the GN) by means of running powers and a new curve at the Swinton end of the line, and when it finally got its cross-country route some three decades later made good use of the facility. And so it continued until October 1968, when Wath Road Jn to Goose Hill Jn was closed to passenger traffic -- not to save track, but because the subsidence slacks had got to a dreadful state and running via Moorthorpe seemed a better option. However, things improved quite dramatically, quite a lot of money was spent, and the line was re-opened in May 1982 not only for Leeds traffic (with some trains turning off to run via Wakefield Kirkgate and Westgate to Leeds) but also for the York traffic via the then-new 60-mph junction at Altofts. This lasted until October 1982 when two things conspired to shift traffic off the North Midland line again. Most important was the desire for rationalisation, and a switch to the S&K would allow Leeds trains to get on to and share the London-Leeds line from South Kirkby Jn and shorten the amount of route needed for the York trains. But there was also a very serious embankment slip near Royston. Eventually funds were authorised to deal with this -- but before work could start the rationalisation ideal kicked in and the job was cancelled.
The full length of the Selby Deviation became available in October 1983, and advantage was taken of the much better route this provided north of Doncaster to move cross-country trains off the S&K to run via Aldwarke Jn and Thrybergh Jn to Mexborough, and thence to Doncaster and York, ginving Doncaster rather than Pontefract a cross-country service. This route was dramatically improved when the Swinton curve towards Mexborough, which had been closed to all traffic in 1965, was restored and re-opened in March 1990.
As a result of the move of the cross-country trains the situation on the S&K was that the southern half saw the Leeds traffic whilst the northern half saw no long-distance traffic any more. As has been said, the timetable was indeed eventually worked out to allow hypothetical working on one line, "saving" Regional Railways the cost of the second line under the rather interesting form of reckoning being developed at that time.
There are still one or two XC trains routed over the full length of the S&K for route-knowledge purposes, and travelling on them shews that this is now potentially a pretty fast route -- but not in my estimation as fast as the Doncaster route. Sheffield to Doncaster can be covered in 19 minutes, given the very unusual luxury of a clear road, and Doncaster to York needs 20 minutes, so with a couple of minutes for a stop and two or three minutes of recovery time the distance could be covered in under 45 minutes. I do not think via the S&K could equal this. For the York trains things could be (but aren 't!) better than they ever have been.
It's very different for the Leeds trains. The present route is not as fast as the North Midland could have been, if the programme of upgrading had been continued as was planned (a new bridge for a straight alignment at Parkgate, straight through lines at Normanton, etc). It was a very well aligned railway that would certainly have been good for 110 if not more. As it is, we get the tedious treck through Wakefield (and the overloading between there and Leeds by local traffic on the inter-city trains). Ah well ....
