The 3.5 DOHC has full round ports in the lower manifold, considerably larger then the 3K upper. The 3.5 and 3.8 SOHC 24V manifolds do have the same ports as the 3K GT upper and that manifold does bolt on to the SOHC lowers. Even clears the COP on the new engines. The SOHC lower will not go on a DOHC engine.
I do not find the 3K manifold to be the proper option for eliminating all the stupid ports on a DOHC. I would have done so on mine. Now this does not mean it won't work.
I have a 3" thick block of phenolic sitting here intending to become a new center manifold and will weld over the side ports of the upper.
Once I have another full manifold in hand I will undertake modding one, might just hack and weld one to get the job done quickly.