It was always part of McLaren's master plan that the Pistols were more than merely a band. In the tradition of situanism however McLaren had intended the film to be a very extreme affair and indeed had begun filming using Russ Meyer, the director of such films as Beyond The Valley of the Dolls (1970). McLaren's choice of Meyer as a suitable director for the Sex Pistol's film is telling. McLaren saw him as '... not being a liberal'. He was a Vietnam veteran who produced sordid and exploitative films and the script McLaren and Meyer came up with reflected this.
I think the use of both past perfect is to emphasize the changement "he had done , thought that before he changed his minds" but what I don't understand is why past simple for came up: is it because he has already had emphasize the changement so he does not need to underline it a new time.Because for me the script they had come up with was before McLaren changed his minds.Or may be it is just after finishing the script(having already filmed some scenes) that he changed his minds.