1) yes, mahogany is a pretty warm wood. I personally love its deep thick warm tone. maple tops add a high end shimmer, so you will have a beautifully three dimentional sound.
2) thats true with any pickup. just because a duncan JB sounds awesome in a les paul doesnt mean it will sound worth a damn in an RG. it may, but it may not. either way it will certainly sound different. although EMGs are battery powered, they still need a decent guitar body to sound decent.
3)maple is warm, rosewood is brighter, and ebony is brightest. but the tonal difference is so small it comes down to cosmetics and feel. I personally like the feel of ebony but the look of maple, depending on the guitar.
4)umm everything from the type of bridge to the type of strings you use.
5) depends on what neck you want on the guitar, almost ever make of guitar has a different neck pocket
I hope this helps!