The alignment holes are not near the transmission. They are in the console where the shifter mounts to the brackets.
Remove the shifter knob and the vinyl surround and boot from the shift console. Look down the shifter shaft where it attaches to the linkage and you will see a hole around 1/8" diameter in the metal bracket. There are actually two holes, one faces sideways and the other faces forward. Move the shifter back and forth slowly and you can see that the hole lines up with a mating hole in the bracket it is next to.
I believe you start with the trans in first gear (not sure though, read the manual). Loosen the cables at the transmission (you might want to mark their position first just in case you get lost in this procedure).
Now move the shifter to align the holes and place a drill bit or other suitable pin in each of the holes. This sets the shifter in the proper position. Now tighten the bolts where the cables attach to the linkage at the transmission. Theoretically your shifter should be adjusted now. I usually have to play with it a bit.
Your problem, though, is more likely at the transmission linkage (at least it was on my 85SE v-6 Muncie 4spd). Have someone sit in the car and slowly move the shifter back and forth and side to side while you look closely at the transmission linkage.
When you move the shifter side to side you'll see that the linkage actually causes a lever (select arm) to rotate causing a rod (about 1/2" diameter) coming out of the trans case to move up and down. The rod has a groove machined into it. A pin on the lever rides in the groove making it move up and down. The pin wears flat so it looks more like a "D" than a round pin. This causes slop between the pin and the groove in the rod which causes the rod not to rise enough to align the shifter forks in the transmission to let you make the 3rd/4th shift easily. Another possibility is the plastic bushings that the lever pivot pin rides in are worn. Rodney Dickman sells excellent replacements machined out of bronze. Look in the transaxel section of his web site at:
http://www.rodneydickman.com/retail.html
Remove the lever that has the pin in it and look at the pin to verify whether this is the problem. To remove the lever you'll have to disconnect the cables from the holder, unbolt the bracket, remove the cotter pins from two linkage pins to allow you to lift the mechanism enough to pull the pin to remove the lever.
If the pin is worn into the "D" shape I mentioned you can grab in in a vice and rotate the pin 60 degrees in either direction to place the round part of the pin back in contact with the groove. If you rotate it 90 degrees you'll get one more use out of the pin. Rotating it 60 degrees allows you to rotate it back in the other direction when it wears again.
You might as well replace tha plastic bushings with Rodney's bronze ones while you have it apart.
I hope I haven't confused you. I'm working from memory since I'm on my lunch break at work.
Good luck,
Carroll