1. A whole lot of custom fabrication.
2. $$$$.
3. A little bit more $$$$.
4. Did I mention more $$$$?
If you're seriously considering a twin setup, then don't half-ass it.
There will be enough clutter going on on the exhaust side...
So, You'll want to go with a Front-facing intake manifold to keep the intake side of the motor....ON the intake side of the engine bay.
At this point, I would not recommend using and AFM splitting to two intakes (per turbo),
But no one said it couldn't be done.
So, something along the lines of MAFT Pro, VPC or some other standalone that doesn't require use of a damned AFM.
There was actually a guy by the name of Yannis here on the boards that was undergoing a 7M Twin turbo setup in his MKII, but last I heard, he installed another 7M in the car and sold it to someone...so I'm not sure what he's done with the twin setup.
Good luck,
Jeff