I had a similar problem with my stock throttle linkage arm over the rear of the header. I was using a stock throttle lever shaft. You know, the standard 1/2" rod bent at two 90* angles. I tried a couple mods of the first one including sawing it in half in the mid-section, sleeving the two pieces and cranking them down with allen head set screws. The geometry was there but the rod was too floppy at the joint to run the throttle dependably.
I ended up getting a salvage pedal/throttle rod at the junkyard. I went and retrieved the cut-up one from where I had flung it in the yard and laid the two next to each other; the new-old piece along side the prototype. As it happened, the failed prototype laid dead flat on my work table. I secured the new piece in the vise and tugged and pulled on it here and there with a steel pipe sleeve. When I was done it was flat like the prototype. I put the solid linkage back in the car and found that the long shank that connects to the carb was sticking up in the air about 20-30* over the top of the header pipe.
I marked the location of the rear pipe with white ink just back of where it touched the header pipe. Then I took the throttle connector rod out and secured it in my trusty vise. Using the steel pipe, I bumped it at the mark with a pipe sleeve and pulled it down the required almount. Put it back in the car and hooked it up with the adjustable stock thottle linkage thingy that clips to the bulbs on the rod and the throttle. It worked just perfectly.
When I replaced the carpet and put in sound deadener, I had to pull up on the gas pedal arm inside the car to get enough throw for WOT. The service manual has specs for the pedal height. You achieve them through fine adjustments to the throttle connector thingy and brute force at the floor. Once again, it works perfectly. You will also have to readjust the kick-down lever on the horizontal part of the rod after it is all working properly, but this is the least of the project. Leave the cable connected and just take the lever off the horizontal part of the rod.
I would suggest that you promote two of the rods though, in case you lose one over the back fence in a fit of pique, or it bends the wrong way. I think I remember something about propane, torch and red at the bend too, but that might have been another project.
Now the throttle linkage rod is dead level across the tops of the header at idle and dives down to the firewall bracket right behind the header pipes.
