Unless there were aerodynamical reasons to consider I'd go for a
very straight tunnel
I looked at Google Maps. You could come out via Ashton-under-Lyne/Guide Bridge/Stalybridge, adding track to the existing railway; tunnel or new railway as far as Meltham; pick up the disused route into Huddersfield just north of Berry Brow. But then someone would want a station stop either side of the Pennines so that, say, you take a fast to Stalybridge and a slow to Mossley rather than a stopper from Huddersfield to Mossley.
It soon gets messy, which is probably why I've avoided most of the speculation and NPR plans. Whatever the outcome, everyone will be disappointed to some extent I reckon.