Hi Basket Case. I've been working on putting my mark D back together for a while now, so I'd also be glad to help. Mine had been stripped down to a pile of bits when I got it and the floor had been seriously affected by corrosion wherever steel underneath had been in contact with aluminium - the two steel cross members (BA45 & BA137) and the points where the flexitors were bolted to the floor were the worst points. Critically, where these surfaces met originally, they were left as bare metal and where the steel bolts on the flexitors went through the aluminium floor, corrosion had turned parts of the surrounding aluminium to powder - you can see the holes around the bolt holes in the photo below. On the cross members, the floor had splits along the lines of rivets. Although most of the floor was perfectly sound, corrosion around the two brake pivot points was also beyond repair and on my car it made sense to replace the floor entirely.
Underneath the car I've used Hammerite direct to galvanised metal paint, but others I've spoken to have used aluminium paint or waxoyl. Almost everyone I've spoken too has used metric stainless fastenings as they're easiest and cheapest to source, use copper grease so that you can undo them if and when the time comes.
For painting the bodywork, you do need to use a good acid etch primer underneath whatever paint you put on top. Aluminum forms a layer of oxide on it's surface and most paints bond to the oxide rather than the aluminium underneath, it'll then flake off very quickly. Some of these primers can absorb moisture though, so you need to check if you can leave it in primer or have to apply the top coat soon afterwards, otherwise you may end up with paint defects.
