[Arran]

Ed;
  The 100 mmf (pF) in the anode circuit of the 6SQ7, if it on the triode or is on one of the diodes? If it's on the triode it was probably for tone compensation, so it wasn't really needed to make it work. On the other two micas, if they were involved in the IF circuits then that could throw the alignment off, if they were in series with the fixed micas inside the cans. The black coffin shaped micas in RCA sets (as well as Canadian G.Es) aren't really that bad in spite of the neurosis about them on the barking dog forum, unless one is falling apart or there is a weird fault I leave them alone, in fact shotgun replacement is more likely to cause a problem then to head off a potential one. That cap checker you have is a reasonable way of weeding out the bad ones, I'm not sure whether it will do it in circuit or not, some will and some won't.
Regards
Arran