Hi, and welcome back to a wonderful hobby!
I must say that you haven't choosen the easiest subject for your return. It's a wonderful model but it takes some work to finish. You might want to take a look at this before you start http://www.internetmodeler.com/1999/july/cars/mclaren.htm and get some useful tips and hints of how this baby is to put together. Now for your questions.
1. You don't need to use the same base coat as MCW's to the other paint brands, I don't use base coat's at all if the surface has a uniform color. Other than on the bodywork.
2. I normally take the parts from the trees, clean them up and remount them so that they woun't get any wounds in the paint whenI detach them again. sometimes I glue them back on the tree otherwise I use blue tack or double sticky tape to mount them on some cardboard, old toothbrush or whatever comes in handy.
3. As for the glue vs. paint it's all the same as in the old days. Paint and chrome must come of before glueing otherwise the parts will fall apart again. I would suggest to build as much as possible in sub assemblies of the items that should have the same color and then paint the whole thing.
For my McLaren I started scratchbuilding the braided hoses because I don't like the apperance of that vinyl stuff that comes in the box.
One very important thing on this one is to study the instructions real close because there is some things that needs to be done in the right order to even get them there. Please keep us updated on the progress, I will have to get mine out of the closet again. Maybe I'll be able to finish it before I get my pension
As I have two little boys taking most of my sparetime it doesn't happen all that much on my workbench.
Good luck!
Niclas