Im in the middle of installing the shifter linkage on the 4 speed in my cuda. The 1-2 and 3-4 operating levers on the side of the transmission have a top and bottom hole that the rod goes through. The rods go in the top hole correct?

They can go in either. The hole closer to the pivot will give you a shorter shifter throw.

Ok thanks. The reason Im asking is because I have them installed in the top holes and when I went to adjust my linkage on the 3-4 rod, the swivel is maxed out, but it still has to thread in more to fit into the lever on the shifter.

Make sure the tabs are installed correctly. They should point straight upwards when in neutral. Put a drill bit through the shifter to hold all of the linkage in the neutral position before adjusting.

Also check to see if your shifter box has shifter stops, they will need to be readjusted also

The stock long snaky looking E body shifter rods will bend making them end up shorter, which will max out the swivels. Use the bottom hole now and readjusted the positive stops with the tranny in each gear, adjust so the bolt barely touches the shifter lever on the shifter and lock the nut down tight Once they get unusable from power shifting you will need to either straighten them back to original and reinforce them or replace them, if you can find those rods now IHTHs

They should look like this.I have rods if you need them.