I have tried EMG's and don't like them. Recorded, they sound great, I did this with my guitar and the pickups I put into it. But standing next to the amp, they lacked the dynamics that the passives had. If I was playing a on distorted channel on the amp, it made distorted amp noises with the EMGs, if I lightened up or hit it hard. With the passives I could, to some degree, control to amount of whomp better with the passives. It suits my playing style better so I go for them. I understand DbU's comment about the batteries, and he is correct. Very little strain is placed on a battery by the EMG's. Nothing like what an analog chorus will do to a 9V. However, I am paranoid about these things as well, so I personally do better without the option of worrying about it.
As far as the woods go, it depends what kind of maple top you are describing. The veneers impart very little if anything to the guitar sound. The caps, like a Les Paul have a larger effect. The one wood that comes up often when describing a Mahogany like sound is Korina. I have a tele made out of this, and it sounds very nice. As far as necks go, the unfinished necks that Warmoth offers are addictive. There are many that are all in the same sort of range as mahogany or maple, and quite a number in between the two. However, the feel of playing unfinished necks is something that can be described as law breaking. Very fun.
Troubled Treble on this board made me a set of seven string pickups for a guitar I have and I love them. They have a lot of detail for fast distorted stuff, the neck pickup has just this great ballsy slank tone, and they clean up incredibly well and sound great for clean parts. I really love the way they sound, the bridge is kinda like a Nailbomb with a bit less mids, and the neck is ballsy without the mud. The neck pickup really makes that position a lot more useful for me. Good luck on finding a fun build.
Patrick