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I have a couple of questions, as I work my way through a first time build. This is for Martin-style D41 kit.

I've seen several posts about using the right kind of glue. This guitar has a 2 part back with a marquetry center strip. I'm not positive what material the center strip is made of, but it looks like decorative wood and not plastic. I was planning to use Titebond glue, like I'm using for the other wood to wood areas. Since this strip is just a little thicker than the back, I will join the 3 pieces together. Does that sound like the correct glue & gluing method? Should I join the 3 with the outside down?

I will use Weld 16 or Duco glue for the rosette, the bindings, and the purfling, which are plastic and abalone. Correct?

This guitar has neck & headstock binding - 1/4" - neck & 3/16" - headstock. The neck binding is taller than the fret board (about 1/32") and a little narrower than the channel between the fret board and the edge of the neck (again about 1/32"). Do I glue in this binding and then scrape the binding down to match the height of the fret board, with allowance for the frets where they meet the binding? Any advice on what tool to use for this? Do I shape/sand the sides of the neck to get it even with the binding? Should the neck shaping be done with just sand paper?

plastic binding I use duco that will do the job

I use a card scraper to bring my bindings down to the proper level. Are you sure you have the correct binding for the fret board? It is a bit unusual for it to be narrower than the channel.

Binding should be set such so you sand the side to mate them and the top of the binding just a touch proud on the top to be scraped flush. I am talking just enough to catch a fingernail.

Checking the size of the neck binding is a good idea. I suppose the binding they sent for the neck could be wrong. The other items in the kit seem to be fine. I checked the other bindings in the kit and none of them would work any better. I'll measure what I've got and then see what else is available. Maybe I'll get another size and see if that makes a difference. I looked at it again earlier today and it may not be off as much as I thought earlier. I wouldn't have to take much off the sides of the neck to get the two to match up. I'll probably have to do a little smoothing & shaping on the neck, anyway. We'll see how it goes.

neck binding is often higher than the typical side binding. The reason for this is the the binding is often heated and bent around the corner and not mitered. I am sure you got the correct stuff. On head stock the binding would need to be trimmed to about 1/8.
On a kit things are a bit large to allow you some fudge room.