To adjust the linkage.
1. Make sure the car can not roll and is safely supported.
2. Loosen the bolt in the Clamp on the shift linkage.
3. Place the shift lever inside the car in the park position.
4. Move the lever on the transmission so that the end that the shift rod connects to is all the way to the rear of the car. There will be an audible click each time you move it but the last click will engage the park prawl and will be more of a clunk. That is park.
Sometimes the linkage has worn bushings so you will need to put a little pressure on the linkage to take up the slack. If so push the bellcrank end of the linkage towards the front of the car while keeping the transmission lever in the park position. The bellcrank is the part going from the frame to the transmission with 2 arms on a shaft.
5. Tighten the bolt.

As for the alignment issues.
Are the bushings good?
Is it possible that your bellcrank isn't seated correctly in the bushings or installed reversed?
Maybe you have the rod inverted on the transmission end?
You are putting the linkage on the lower ever correct? The upper lever is commonly called the kick down linkage that connects to the carburetor.


Hope it helps.