Well I believe the 99 full size trucks are built like my 99 Dakota frame is meaning that the front and rear frame sections are riveted together just ahead of the rear axle hump, as well as the front spring hanger is riveted thru the overlap section. Mine isn't as bad yet as some I have seen but the rear frame section likes to rot right behind where it overlaps the front section. What I would do would be to cut the donor rear frame section just ahead of the overlap and grind/cut/drill out the rivets holding the 2 sections together, inspect and coat the parts of the frame that butt together to form the overlap and bolt it back together.
I think that the op is talking about something similar.
Whether STD cab, club cab or short/long bed later in the truck's series I believe that they all used the same "butt" portion of the frame, with only the front portion changing between trucks depending on cab/ bed length combo.
(And yes before anyone asks yes I know that the Dakota and the full size frame won't interchange but by this time they were building both series of trucks in the same manner)