There shouldn't have been any problem. Your vehicle is a 98 EB just like my wifes and I didn't have any issues. I used this harness that is for Ford Premium Sound systems
Metra Part # 70-5600 | Ford wire harness | Metra Online
I am willing to guess they used the wrong harness or something. My '03 had 2 harnesses in the back of it, like the '98, but when I put an after market head unit in I only reused 1. But one harness, the long flat one, had all the connections for power and such, and the shorter one had all the connections for the speakers. The green one has the 8 wires for the four speakers. Is this the one that had only two sets or was it the harness that plugged directly into the back of the radio? If it was the one from the radio then it may be the radio and not their work, but I don't see why the radio would have settings for an output it doesn't have.
Do you have a model number for the radio? There may be a limiting factor in the radio, but shouldn't be. It should send the low level input to the door speakers and still send a signal thru the RCA cables to the amp for the sub. I am not seeing a reason it shouldn't work.
Victor
I wish you were closer, I'd have you come over and we'd just fix it ourselves. Can you remove the dash panel to get the radio out? If so I would love to see a picture of the kind of harness they used. Just pull the radio out and snap a pic. If you're not comfortable doing it that's ok. Did it work in your brother's truck just fine? It may be the head unit that is limiting this.