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I also like the clutch linkage hole, I switched to automatic trans so I didn't need it and the hole is big enough to allow the big end to slip right through. I did it this way because it cleans up the engine compartment a bit and lines up the speedometer head with the cable a little better and this will reduce needle flutter on a used cable. I used some silicone to hold the cable to the firewall under the carpet. This routing gave me a little more cable to make a nice big sweep to the tail shaft again reducing sharp turns too reduce flutter. Later model cables are somewhat shorter than the originals and I suspect that explains the clutch hole routing used by the PO. On the firewall above the rectangular bulkhead connector you will find a big round hole, about 2 inches in diameter, thats where the cable exits the firewall, passes to the outside of the steering column and along the frame and then over to the tailshaft. I use wire ties to keep it off the exhaust. Actually I think the cable could share the clutch linkage hole with a little work to keep them seperated so using the clutch doesn't wear the cable.
There is supposed to be a smal rubber coated clip screwed to the floor board under the truck to hold the cable away from the clutch linkage. I think Williams idea is good if an auto trans is used but if you must run the OEm linkage, route the cable from the speddo head, out the hole in the firewall, throught the rubber clip, down the frame (use clips) and into the trans. Should net you a smooth flow without any kinks or binding.