I had the exact set up that you are talking about but no tremolo. I had a Washburn X-50 Pro with the EMG 81 & 85. It had a soloist style mahogony body with a clear coated flamed maple top and ebony finger board with no inlays. It was a sweet axe, but I found that without any inlays I was getting lost on the fretboard, so I got rid of it. Sounds a bit ridiculous, but we guitarists are a strange, quirkie bunch. Well, at least I am....
The pickups sound great when they are distorted, especially when played loud through a hi gain amp. But when you back down on the volume to play clean the guitar sounded lifeless to my ears. For whatever reason I couldn't hear the tone of the wood through those pickups. It was really weird and kinda tough to explain.
When the guitar was played unplugged, I could hear a really sweet tone coming from it. The whole guitar would ring and I could feel the guitar vibrating in my hand and against my body. It was so cool sounding. But when I plugged it in and played it through a clean channel, something was lost. It sounded like those pickups sucked the "life" and tone outta the guitar. At least to my ear it did.
I traded the Washburn in for an Epi Les Paul and swapped the pickups for a Seymour Duncan '59 (neck) and a JB (bridge). I can get sweet clean tones with this guitar and some pretty crushing distorted tones. I'm very happy with these pickups and would recommed them to any one who is looking to upgrade.
You also have the option of dual to single coil switching that you do not have with EMGs. EMGs are also abit more pricey and you have to be very careful about keeping a battery with good charge in the guitar. You have no way of knowing how much battery life is left in them until they stop working, which could be disasterous if you happen to be in the middle of a show when it happens.
Ultimately the dicission is yours. You could also check out a couple of the other threads on this site for some insite from the other guys. Look in the pickup section (I think). There is a pretty big discussion on this topic there about actives versus passive pickups there.
Hope this helps and post pics of your build when its done. Everyone here would love to see it, no matter what pickups you choose...