Stopping the high speed line at South Parkway (itself not the easiest location to reach) would probably just move the logjam to the Edge Hill end of the WCML. I'd suggest a high speed tunnel to there, then take the local services underground via the old freight tunnels, clearing Lime Street high level for high speed and other long distance trains.
Leaving the transpennine lines as they are would be idiotic, though that's no gurantee it wouldn't happen. The Standedge route is full already, and Hope Valley is close to it
I disagree because there is only sufficient demand for one new tunnel and that should be to divert city line services into Liverpool Central as part of Merseyrail. The tunnel required would be much shorter and not need to be built to support high speed running. The 4 tracks from Liverpool South Parkway can handle more traffic and Lime Street could handle HS2 and NPR services if local services went to Liverpool Central e.g. 2tph Wigan, 1tph Warrington BQ, 2tph Crewe (replacing Birmingham services).