I had no problems at all, but I had noticed for awhile the cracked wiring. CEG gave me the info and I met the under 10 year, 100K mileage limit. So I took it to Ford and the shop manager came out. He looked at it and I brought it back a day later and left it with them. Got a loaner fully loaded Taurus too (I miss that car).
They had it so long because
1: The harness is special order
2: Time intensive job
3: With my loaner I told them to "take their time"
4: I think in the install they had a bad connection somewhere and when they were done the car ran like crap. Changed TPS & engine PCU (Is that what it's called) and that seemed to do it.
I got it back and it ran fine for a week, but unknown to anyone a tech had left a battery wire rubbing against the EGR tube and it got hot, melted the plastic coating and arc welded its way through one of the little tubes on the EGR tube and killed my DPFE. So I had Ford replace that and I bought a new DPFE and cleaned the TB.
Since then I've replaced the coil & spark plugs (not sure if the harness recall killed them or age) and I've had no problems since.