What are you going to be putting the BMW drivetrain into? I couldnt seeing the 850's drivetrain fitting into a mid-engine replica due to its lenght...
I own a BMW 850i (auto-trans) and can tell you that the engine managment has almost two of everything and is pretty picky. Tons of factory wires and sensors that would much more difficult to swap into something else. Unless you are dead set on the BMW V12, I would recommend going with some other option for a drivetrain. Athough the BMW v12 is a good motor it just doesnt have the power that most people think it has. The parts are super expensive, and the performance upgrades are limited and even more expensive. In the end it doesnt really sound like an real Lamborghini V12, I have heard some v6's that sounded closer to a real Lambo. If you could get the BMW V12 and BMW trans to fit in a mid engine replica, the cost for a stand alone, custom axles, brakes, suspension, tuning, exhaust, ect, would cost alot... Not even taking in consideration any parts like waterpump, distributor caps, spart plug wires, ect that needs updated/replaced at the time of swap....
Im running Microsquirt on my LS4 and a stand alone trans controller for my paddleshifted 4t65ehd in my Lamborghini Diablo Roadster replica which was way easier (for me) to use than using the factory LS4 ecu and wiring harness. So to me it would make more sense to look into a stand alone managment system.
I would recommend looking into this:
http://www.diyautotune.com/ms3-pro.html to run the BMW V12, but it comes at a price and not much if any support to aid you in getting it to work on the BMW V12.
Im not trying to discourge you in your quest, Im just trying to relay my "thoughts" from someone who has been there. As a person who has built a replica, I know what it took for me to complete mine ($$$) and not get overwhelmed and loose interest after you get started and end up with a unfinished project and $30k or $40k spent that you will never get back.
My advice- get the best replica kit you can, its going to cost more in the begining but be so much more worth it later in the build. Find a decent Fiero or other decent donar, find a good 3800 v6, either with the supercharger or perhaps add a turbo.
The aftermarket is very large as well as support with the v6 and much cheaper to build. Put all the money your going to save from the v12 and put into bodywork, paint, interior,ect, you will have a much more reliable, powerfull, and most important- a completed project sooner. And with the right exhaust on the 3800 a great sounding ride....
Just my opinion~