Not sure what you mean by, "shifter box". Your transmission is a 4-speed Top Loader. it's a great trans and by no means a one-year-only.

The shifter linkage is a different story; often called a "Broomstick in a barrel." It was so loathed Ford went with a Hurst linkage the following year. While not good for bang shifting, the 69 linkage is functional. Likely your shift linkage requires new bushings, lubrication and adjustment.

It is possible your Top Loader is simply worn out and requires a rebuild. If that's the case, it's no big deal. Parts are readily available. Any transmission shop can rebuild it or, if you're ambitious, you can find videos instructing you how to do it yourself.

 

Have you already tried re-aligning the shifter arms in the gate? I think the shop manual has a good explanation of the process. Lots of threads on this forum outlining the process also. I started having the same problem you are and re-aligning the shifter fixed it.

 

First step is to check the adjustment, and inspect the shift rod bushings. If that's all good, then a rebuild of the mechanism may be in order. Kits are available from any Mustang parts vendor. If you don't feel comfortable doing it yourself, Bill Healey is widely regarded as the master of the Ford shifter mechanism.

The Hurst is a great shifter, but they are now in the $700 range for new setups.

 

Bill Healey is the final destination

 

If you have a stock 69 4 speed shifter it is a one year only shifter. Good suggestions on checking alignment and bushings. The fatal flaw in that shifter is the reverse detente assembly and Bill Healey is the man to speak with. The stock shifter rods and tabs are stamped with part number/ID's. You might check to see if you have the correct Reverse Rod and Tab ? The correct Reverse rod is stamped C9ZA-7B112-B and the Tab is C9ZR-7C165-A. Verify that the other two rods/tabs are correct ? Brian