I think I can answer a few of these!
Was John Paul Jones wearing a wig in the TSRTS?
Yes.
Subsequent filming and release[edit]
Dissatisfied with the progress of the film, Grant had Massot removed from the project and Australian director Peter Clifton was hired in his place in early 1974. Massot was offered a few thousand pounds in compensation. Peter Grant later sent someone to Massot's house to collect the film. However, Massot had hidden the film elsewhere and so instead an expensive editing machine owned by Massot was taken as collateral. Massot served a writ, leading to a period of stalemate which was finally broken when Grant and Led Zeppelin's lawyer Steve Weiss agreed to pay Massot the money he was owed, after which he delivered the film to the band. Massot was not invited to attend the premiere of the film at New York but he attended anyway, buying a ticket from a scalper outside the theatre.[3]
Clifton, realising that there were crucial holes in the concert footage, suggested that the entire show be recreated at Shepperton Studios in August 1974, on a mock-up of the Madison Square Garden stage. Close-ups and distance footage of the band members could then be slipped into the live sequences, which made up the bulk of the concert footage seen in the film. When it was agreed that the band would meet at Shepperton Studios for filming, Jones had recently had his hair cut short, so he had to wear a wig.[3][6] Robert Plant's teeth had also been fixed between the 1973 and 1974 filmings.
https://en.wikipedia.org/wiki/The_Song_Remains_the_Same_(film)#Subsequent_filming_and_release