Sorry, I am really pressed for time nowadays, but I'll try to help;
The top photo shows original Feifel tubes. Note the faceted surface and slight twist.
The bottom photo is in Bovington museum, and is so similar that I think it's an original tube; can anyone confirm?
If so, you can see that it's made of faceted metal, not fabric. There are other tubes on the Bovington tank that have a plain round cross section; I don't know if they're original either.
I don't know of any photos where the pipes were removed and the filters not; so, I assume that they were connected.
The coax MG must be removed on a Befehlstiger. In the case of an old "flat" mantlet being used, this would be a Tiger (P) mantlet converted by having a plug welded in. It might be a good fit or it might not; if there were no Zimmerit, you would surely see signs of the plug.
The RHS would have a ceramic pot countersunk into the hull roof. I don't know a good photo of this, but the Dragon kits represent it quite well;
The rear antenna tube was on the left for S04. It was on the right in Tigers with an engine heater, i.e. Lates.
The episcope was connected to the 2 small holes above the driver's visor, this did not affect the visor itself.