This stuff I learned the hard way on this Flanker two years ago...and I am far from an expert in these matters.
Gloss black or a darker grey ought to be OK for your base for either MM metalizers or Alclads. Since you gradually build up the metallics, it is up to you. I put the metallics on too heavy (a combination of MM and Alclad) , so the base color was moot in my case. Heck, go nuts and use a variety of neutral colors on the different areas and see what happens!
Tamiya tape doesn't do Alclads or MM Metalizers any favors- in fact it melted into the paints for me, even after letting the paint cure for a few weeks before masking.
It seems that the best thing (for me) to do is to work on the engine panels last, after all the other camo painting. It is a big ole PITA to mask those panels out afterwards, but that should dramatically lessen the chances for errors (knock on wood).
Yes, lacquer thinner for Alclads- I use just a little to thin them out so I don't lay down too much to start with and then blast a larger quantity through the AB to clean it. I'd also field strip the AB afterwards and detail clean out the remaining gunk so the lacquer thinner doesn't melt the seals.
Among all the issues surrounding Flankers, these engine panels seem to be the Achilles' Heel. This was my first effort, using Alclad steel on the forward panels and MM Titanium on the middle panels over MM gloss black. It looked good until I tried to mask this for the rear-most section.
hope this helps!