[JVM225]

Just changed my shift cable.
Probably easier for you to install the shifter end if you disconnect the cable from the transmission first so you don't have to fight it.
Put the car in park.
Remove cable from shift lever on trans by removing pin and pulling it off of stud, then remove U shaped retainer clip from bracket back where the back of the rubber accordion shaped boot sits.
Once the U shaped clip is out, work cable out of bracket on transmission.
Head back in to passenger compartment.
Feed the cable up through the holes you mentioned, move the shifter all the way to the rear position. Secure with clevis pin and cotter pin, then secure the cable with U shaped clip that goes up against the hole you mentioned that is closer to the firewall.
Once it's secured properly inside the shifter, put the shifter in the park positions, go back under the car and reverse procedure to re-connect cable to shift lever on transmission.
Make sure rubber grommet that seals the hole in floor is properly in place, and you're done.