I do not believe that the interworking will continue, assuming the paths through Bolton and Manchester have to remain unchanged. As I explained in the 769 thread:
That means three additional diagrams, relative to the six currently needed for the interworked Alderley/Stalybridge services from Wigan. Curtailing the Leeds and Blackburn services to Wigan will only save two diagrams, because the timings will not permit them to be interworked.
If the 769s are not in service by the end of this year, Northern will be at least 32 (8*4-car) diesel carriages short of requirements. So I concur there would then be a strong case for temporarily retaining a few Pacers, plus the 20*153s.
I really, really can't see Pacers staying on after 31st December, it would be politically suicidal.
As for the number of DMUs needed, remember Northern essentially saved one unit by curtailing the Kirkby services at Wigan. There are now two, 2x2 car diagrams where there were 3x2 car diagrams, with 1 x 2 car diagram shuttling Wigan - Kirkby (I think I've got that right!). So, there's an extra unit there to be used, which added to the two saved from the Leeds/Blackburn runs should make the switch neutral in terms of the overall number of units needed.
Of course, it does mean that the consistent offering of the 769s on all via-Bolton services will now be impossible as there won't be enough of the bi-modes to do it with... but that's just another example of allowing the self-interest of a small group of passengers (Southport commuters) to override bigger issues, in my opinion.