Something to think about when working with aluminum: All aluminum products get the majority of their strength from heat treatment. When you weld aluminum, it looses ALL of it's heat treatment in the heat affected zone around the weld. This isn't a huge problem when you weld on an intake(or any other casting)as it's probably not tempered to begin with.
I don't know if the OEMs heat treat after final welding, or just size the aluminum components to be strong enough in a "T-0" condition, but you may want to find out which before you cut down and weld a factory aluminum shaft.