Hi Dee Bee,
As far as removing that "Nut" and not a bolt is concerned it is usually done with the chains still installed and the clutch in the engaged position, but as you've already pulled that part of the drive train apart all you need to do is lock up the reel with a suitable piece of timber through it and place a 3/4 size socket on a breaker bar over the nut and give it a sharp blow in the traditional anti-clockwise direction and it should come off easily enough. You could also use the ring end of the combination spanner you have there (not the open end) if no socket and breaker bar is available.
Yes the height adjuster should be straight, so placing it in a suitable vice crosswise (horizontal) with the bent section being exposed at the end of the jaws of the vice. Now again using a piece of timber to protect the thread area use a hammer and tap it back into line. Protecting the thread is paramount here.
Now those last two items consisting of rubber and odd sized set screws are definitely not genuine Scott Bonnar parts. (nor Rover) I have just looked back at your photos and as I suspected they are bodgey catcher rubbers that have been attached by a previous tenant, regardless they belong in the circular filing system and new ones must be sourced. Could you please supply a photo of the area from where they have been removed as that will give me a bit of historical evidence if that machine used the push on type rubbers or the later replacement bolt on type.
For now,
Cheers,
BB.