Yeah ford harnesses suck! Here's the way I think it goes...
Not sure on pre 1998, 95 96 and 97 may be the same as 98.
98 and 99 dash harnesses are different because of the location of the air bag control module. On 98's its under the ps kickpanel. 99 under the cupholder/console.
99 & 2000 is different because of the reason you found...the big square plug behind the dash for the frame harness. (but may be usable if you change the harness that goes down to the frame.)
98 underhood harness is different than 99 & 2000 because 98's have crash sensors mounted on the core support. 99 & 2000 are the same.
2000 & 2001 is different because the changed plug ends to go with the updated pats system. Under hood harnesses is different too.
In 2004 they changed again to a completely different harness with different plugs/fuse boxes/ and pats.
I converted a ranger to a power window setup by adding the wires to the harness from a donor harness...not fun but it worked. You also need to either run a wire to the under hood fuse box or change that harness too.