I see the date of the original post but didn't see the question answered. The shift on the fly refers to a transfer case that can be shifted manually/electronically from 2H to 4H and from 4H to 2H without having to be at a standstill, in other words while you are driving at speed less than what maximum speed is for engagement. Another style of transfer case that is not shift on the fly would be an AWD one, I know some Ford vehicles do come with all wheel drive transfer cases.

Programming a PCM without being able to 'inhale' the already stored configuration means that you will have to input it all manually and defining wether the vehicle is a [{manual shift on the fly}, {electrically shifted}, {4X4 or 4X2}].
Then you have to further specify based on your previous selection if it's; [{4X4}, {AWD, 4X2, or not applicable}].
It's sounds more complicated that what it really is, really straight forward.

 

The transfer case grinding and clunking when it's being shifted on the fly during normal driving and not when stopped would mean there is something wrong in the meshing mechanism and would most likely required to be opened or perhaps inspected with a camera scope.

 

No, the ford manual states: "When shifting from 2Hi to 4Hi "on the fly" some sounds coming from the front differential is normal operating procedure.

 

Oh well yeah naturally. Maybe his grinding and clunking is different than my grinding and clunking lol

 

as long as the grinding and clunking is a few seconds when switching to 4wd, your good to go.

 

All the manual transfer case 4x4's I've ever used (except the older F250/F350 with the manual locking hubs), you can do this. Heck, even my tractor lets me shift into 4x4 while moving pretty quick.

 

Even the F150's with the lever instead of the **** are electrically engaged. The days of true manual transfer cases are long gone.