well, the fuel lines run over the transmission end in a 996, and if you put a 996 intake on a 986 you have to reverse the whole intake (to get the TB over the transmission end) so the fuel lines will be in the right place when all is said and done. you'll have to figure out how to adapt the 986 fuel lines to the 996 rails - porsche looks to use 1-time barbed fittings, but i've read that with heat you can get them off with no damage and then just hose clamp them when reinstalling (perhaps with some fuel-rated thread sealant?). you'll also have to extend your brake booster vacuum line to the other end of the engine.
you'll have to take a hard look at your head; here's a good pic of a 996 manifold; i think you'll find that there is no spot on the head to drill and tap in at least one of the required locations:
https://www.ebay.com/itm/99-05-PORSCHE-911-996-CARRERA-LOWER-INTAKE-MANIFOLD-ADAPTER-PLENUM-9961101017R-/291880861094