No contest there for me. Absolutely I'd clip two plugs and solder one in their place vs. ripping out and replacing an entire engine harness. What kind of question is that? lol
Of course, if you think it's hard reading and understanding a wiring diagram and you don't know how to do a good job at soldering or don't have the right tools...well, actually, then shucks, you shouldn't really be swapping a harness either. That'd almost be like tuning and repeatedly blowing up customer cars without understanding a compressor map, but, you know stuff like that goes on every day.
edit: And I've SEEN a harness so I guess I'm qualified craig. Here's what a full 9-5 harness looks like, without the engine harness