It's a great idea to use those TBs. I have a set of Keihin 38mm bodies (from a 2006 R6) that made me think along the same lines. It's too much work for me though. They'll flow just fine and even use a very compatible Bosch system. Bore spacing and linkage modifications will be your big problem. I'd get the M42 manifold machined to accept the TB boots that many motorcycles use. You'll need an aftermarket ECU as well, like MegaSquirt.
I'd stick with Bosch, but not necessarily BMW. FI systems from Bosch or Siemens are just a commodity, basically. One size fits all.
IMHO it'd be FAR easier to wire the aftermarket standalone first, get it working with the stock parts, then do the radical TB or turbo upgrades.