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Are you sure the flickering lights aren't because of the old harness shorting out or having a bad contact some where causing them to flicker?
I would assume a new harness would fix this.
Sounds like you got a short or a loose connector some place. A new head light harness "should' fix it. Unless you want to take the other apart and look for the problem.
My headlights were flickering & it was the headlight switch.
Maybe turn your lights on & shake the **** & reach under the dash & shake the actual switch & see if they flicker.
I'd also make sure the fuse is making good contact in the fuse block. I had that problem on my cig lighter, it would come & go. Bent the brass pieces that actually hold the fuse to make it tighter & problem went away.
If thats the case then it is either bad wiring, bad switch, or just a bad connection. Actually, It could just be one headlight doing it. If thats the case it could just be a bad bulb.
Sounds like you either have a bad headlight ground connection or a bad switch. You might want to check the wiring going to the dimmer switch. I have seen it where the insulation would rub through and the wires would short out on the floor board.