If the body shifted enough, it might be interfering with the shifter, but that would usually mean just a little grinding of the sheet metal. Not sure about the '66 style shifter though.
Is this an early model with the round boot, long lever and simple round knob? Or the later model with the plastic housing cover and T-handle shift?
Are you sure the body lift was the 1" type? The standard cushions/insulators would be 3/4" tall, and the lifted ones would be 1 3/4" tall.
What's it doing that you feel you need to adjust the linkage? It might have needed it anyway, as it is pretty old now, but if the body is interfering, you might as well make the tweaks needed to get things working perfectly again.
Your clutch pedal rod might need some lengthening as well, if it was not done at the same time.
Is this a 6-cylinder engine or V8?
Sorry for all the questions, but since this is your first time here, we gotta' get to know you a bit.
And speaking of which... Welcome to classicbroncos too!
Paul