from the tech library, the 3.0 underwent minor revisions up till 2001, after 2001 they are all the same....
The 1991-2009 Ford Ranger 3.0L V6 Vulcan engine is a 60 degree V6 engine that replaced the 2.9L V6.
www.therangerstation.com
I think you are well past the PATS 1 to PATS 2 switch, so both should be PATS 2
are you maintaining the same trans? (auto trans computers throw a fit if they can't see the trans connected when you swap to a manual).
I've never touched the 3.0 so I'd definitely wait for someone better qualified to answer...
and just a sanity, check they are both the same 3.0 motor right, neither of them is the 3.0 ecoboost (entirely different animal)
yes they are both the same transmission and engine type (3.0 vulcan) both are RWD as well, i do know the MAF if different, although i can swap my air intake tube and filter housing with the maf still attached, as for o2 sensors and camshaft, crankshaft sensors they all seem to be the same as well