You stated that the linkage worked fine with that linkage pin and the only problem was the pin length was too short to allow the retaining pin and washer on the outside of the bracket to secure it.
Nothing says the retaining pin/washer needs to be at the far end and you should, even if the pin in is case hardened, be able grind a small flat spot on the shaft just inside of the bracket arm adjacent to the integral nut. As there is little to no stress on the shaft from normal operation of the linkage, doing this won’t affect anything. You can then secure the shaft centered in a drill press vise and drill it to accept the retaining pin at the flat spot you have just ground in. Just don’t forget to center punch it to keep the drill from wandering and give yourself enough clearance from the hole you drill to the bracket arm to keep the arm snug to the integral nut with a washer or two. This is not critical, it only needs to be tight enough to keep the pin engaged in both sides of the bracket.
That integral nut is there to allow torquing the shaft to the block or bellhousing boss. If it bottoms in the mounting hole before coming up to the appropriate torque, you can strip threads or crack whatever it goes into. DO NOT reef on it, instead use a flat washer or washer stack to allow it to come up to torque.
