The 96s have inferior traction equipment to the 95s, being an earlier design similar to the GEC Networkers.
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Replacing the Jubilee Line trains will mean replacing the platform edge doors also, unless the train door openings are in the same place, which will be a major additional expense.
Two option:
1. Modify the bodyside design of the new trains as required to suit existing openings.
2. Replace platform edge doors to match a standard train design.
I don't know how far out of alignment the doors of the NTFL design would be, as being manufactured for the Picadilly Line, but the design might have been conceived with different car length and door spacing in mind for subsequent series builds, so cost may not be insurmountable.
The existing doors may require age/condition-based renewal anyway after a long intensive service life, so it might be possible to rebuild to a different spacing at little additional cost. Even if this was the case, changing door spacing would still be difficult logistically as all sites would have to be complete before the new trains could enter service, and no old trains could run after the first existing installation was taken out of use, unless TfL could get short term derogations to run temporarily without screen doors during a construction period, which I think is highly unlikely.