My questions are :
1. What colour should I paint the interior of the door and skin over the light grey epoxy to look as per factory ? Matte black or?
Since no one will ever see it its best IMHO to get a good coat of paint to reduce the chances of future rust developing. a semi-gloss black would be just fine
2. I will apply spectrum sludge sound deadener onto the inner door skin as per the layout on my old skin which was just in the middle section correct ?
That is what I see in the originals
3. What should I paint over the sludge and colour if anything (see pt 4) ?
You can wait to apply the semi-gloss black to the interior of the door until after this step so that everything gets covered or simply just apply a second coat
4. I am assuming that overspray from inner door inner colour (which is black on my car) would just have overspray that will go onto the inner door and skin through the gaps and cover the sludge and thats it ?
Yes so that the semi-gloss black applied earlier will all just blend in and if you do the mask and the open center the exterior spray will just flow into and over some of the surfaces lightly
5. Door Flanges need to be seam sealed BEFORE skin is attached and bent on?
That appears to be the factories practice at the time
6. Any suggestions on what to use on the horizontal beam to attach it to the skin and should I apply the staples back as nobody will ever see this ?
I would use some structural adhesive to service a similar purpose that they used to bond the outer skin of the hood and trunk lid to the inner structure. Only much stronger