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You can use the wires that go through the firewall that DetailerDave mentioned, you can use a grommet like Chris said, or you could drill your own hole like I did when I installed an EGT, boost and fuel pressure gauge. I went through just behind the brake pedal because I have a ZF6 manual and did not have the clutch lever plug in the firewall.
Easy to do once you get past the planning stage of the install.
In addition, I used a small hole near the foot well on the passenger side to run my A/V cable for my backup camera. There was a grommet already there and I simply went through it after securing the cable to the frame from the rear of the truck.
Just get under there with a flashlight and have a look.
There is also a hole/grommet on the driver side floor. You can see it from beneath the truck. Just pull the weather stripping back, pull trim off, and pull the corner of the carpet back. I went through this hole when I wired my reverse camera. Avoids the hassle of getting the wire through the firewall and back under from there. Some back-up cameras don't have a lot of extra wire, so this shortens the path a bit as well.
In my 2002 F-250 XLT SD I was able to run wires from the cab to the engine compartment behind the driver side A-pillar cover. The wires pass through right on top of the inner fender. No drilling, grommets, etc required.
Thank you everybody for the input, this was great help in locating a usable hole that's already there.
I ended up running my backup camera and 5 additional wires through the existing hole using a new grommet for wiring on the driver side and some butyl to seal it. This way I was able to run the wires from 3 of the upfitter switches out as well as the wires needed for the alarm and the backup camera.