Check to see if you have power at the end of the factory harness where it plugs into the HIDs. If you do, I'm thinking they reversed how the plugs join. I know that a least one of the popular HID kit warned you to not go by how the plugs would normally connect because the HID harness wires could be reversed. I had that this issue after the recall and the dealer said they never touched the wires, which proved to be a lie after I finally remembered the wire were reversed. Hope this helps.
The recall harness is after the fusebox, when powered up, the fusebox relay feeds power to the fused portion, the bypass kit replaces the fuse in the the fusebox with a inline fuse and a switch whereby you can 'break' the circuit preventing the lights to come on. Since I put a regular fuse in, that negates the bypass harness entirely and since the lights came on, the wiring on the harness plugging into the HID's was correct and I also verified it.
Now for the good news! Fricking spade connectors and electrical crap. You mess with them, move them around and flakey things start to happen. I disconnected all the connectors on the bypass harness and crimped the female connectors down further with a pliers and reconnected everything, walaa! It works again! Which connector was flakey, hell I don't know. I just wanted them working again until I get the time to redo the bypass thing by subverting the grounds on the feed relays. I'm not impressed with the rinkydink way the bypass harness plugs into the fuse holder, so doing the relays instead will take care of that.
Thanks everyone for the help, just letting me vent and bounce it off others helps me troubleshoot sometimes and work the problem.