[The Radium King]

airbox - 987 is the ticket.
maf holder - depends on the tune you are running. 99x - use a cayman maf holder. 986 - saw the old one off your current air box and adapt it to your new airbox. I had a bmw maf holder in my hands and measured it; it looked to be a mm or two off the oem unit. 2 mm is over 5% difference; your ltft can only manage a 20% cumulative change in closed loop, and trims don't even apply when running open loop which might result in running leaner under load (not necessarily a bad thing for power and fuel efficiency, but perhaps stick with the higher octane fuels).
plenum - 99x. I have not held them side by side but 997 looks to have slightly better design. regardless, either is an improvement over 986. 987 has a flapper valve in it and probably best avoided.
throttle body - cayman or 99x. gt3 is bigger, but *I think* just gets necked back down at the 99x plenum so no gain unless you go to an ipd plenum (gt3 plenum is part of the manifold and the manifold is designed for the metzger engine so can't be used in our application).
intake manifold - if you want to use a 996 intake manifold on 986 heads you'll have to tap a couple of holes and build brackets for a couple more. everything lines-up otherwise. x51 intake is a little lower than base 996 so might fit a 986 without lowering the engine. 987 engine cover should help also.