Taking nothing more than a cursory glance at the TPE timings through the core, it seems to me that the problems with the timetables are not just centred around the Manchester / Ordsall corridor. Many TPEs are losing time through the York-Leeds-Manchester section, and with such tight windows at Manchester its not surprising that even a few minutes lost causes so many problems further along the route. And this is nothing new BTW, on the previous Scarborough-Liverpool path that I used regularly between Leeds & Manchester it was not unusual for it to lose 5-10 through York, more through Leeds-Huddersfield & then lose its path across the throat at Mnachester Piccadilly. Even if it was on time, it was not unusual for it to catch up with a Northern Huddersfield-Manchester stopper running late, and lose similar time by the time it got to Ardwick.
Herein lies the problem, the North TP is too busy, & too capacity limited to act as an Intercity, Regional & Local line. There just aren't enough overtaking points, and those that exist are too short to really allow smooth running of all types of services. But being one of only three cross Pennine routes, all with the same problems, it has to serve as such. So what is needed is real investment, and that needs to start soon. The D(a)fT & Grayling have procrastinated about what to do for way too long, real solutions need to be mapped out & put into play post haste. Given the mounting problems with track capacity, demand, platform lengths its never going to be easy, and may well have to include both short & longer term plans to get it working. For me electrification of the North TP & Leeds-York, and dare I say it straight after if not alongside, the Calder need to be funded & planned to allow for better acceleration profiles for EMUs / Bi-Modes across the North TP to allow better chances of timetable recovery, with the (eventually) Calder available as a contingency. Then as this rolls out the digital signalling indicated as an option by the DfT can be rolled out to increase track capacity. Finally, and as a longer term plan a new route through the Pennines to eventually remove the InterCity element from the North TP completely.
In the meantime? Frankly I don't know what the answer is. Perhaps once additional DMU availability opens up with cascades from other TOCs, Northern could sub-contract the stoppers once again, splitting them at Huddersfield to reduce impact whilst TPE use some of the capacity released to strengthen existing services until the new stock comes online, with the rest used on supplementary services such as York-Scarborough as & when needed.