Manual Transmission Problem
The original owner moved the 3-speed column shifter to the floor, could this be the issue is it more likely inside the transmission? Any help or guidance is greatly appreciated.

My comments are directed at the Ford 3.03 Light and Medium duty transmission. That is what is in 65-66, I am not sure if 1964 is the same, so if this is not a good assumption, I know garbz2 will chime in and rescue me.
After that disclaimer: If the levers on the transmission or shifter do not allow enough movement for the transmission to go fully into gear, it will pop out.
There are stops on the floor shifter mechanism that can be adjusted, or I suppose it could be the shifter rods not adjusted properly or just a problem with the floor shift installation.
You can crawl up under the truck, disconnect the offending shift rod and see if the lever on the transmission is completely engaged (you will be able to see and feel it move it further into position).
If it pops out of 3rd, then the front transmission lever may not be going forward far enough (shifting into 3rd causes the mechanism to push the 2/3 transmission lever forward). Once the shift rod is disconnected, see if the 2nd/3rd transmission lever will move forward more.
If that doesn't fix the problem, then the transmission itself is the culprit. Remember this is a floor shift, so column alignment/cab should not be the issue.
Has one brass syncro blocker ring on 1st gear syncro, two brass syncro blocker rings on 2/3 syncro.
The teeth on the blocker rings wears down, causing the shift lever to pop oughtta gear.
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As original: At the bottom of the steering column under the hood are the two manual control selector levers that the shift rods from the trans attach to.
In each lever is a bushing and insulator. 1961/64's use different bushings than 1965/72.
The bushings age crack, and/or fall apart. Now the shift lever will bind up between 1st and 2nd.
Peeps are unaware, or cannot find the parts. So what do they do? They install a floor shifter.
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The base metal shift collar has a bridge inside the column that connects it to the shift tube. The bridge snaps, the shift lever flops around.
Same scenario applies, peeps don't know where to find one, so they install a floor shifter.
Meanwhile...back at the ranch, all these parts can be found NOS. The 1961/64 bushing (kit-C3TZ-7343-A) is available from Ford. The 1965/72 bushing (kit-C5TZ-7343-A) was just obsoleted this year as was the 3 M/T shift collar.





