The column has nothing to do with the shifting of the t-case. I still have my auto column in my truck, and all I did was take the shifter off, replace the column covers with the manual column covers, and put the blank coverplate over the gear indicator on the dash.
That being said, you must have the tranny is neutral (as far as I know) and the clutch depressed, in order for it to go into 4low. Unless the guy never worked on the clutch pedal, in which case the truck thinks the the clutch is always depressed, and it will even start with the clutch out, in gear (like mine).
I think you're problem is electrical. I can't remember what I did, but when I did my swap, I had a problem identical to yours, it would go into 4wd fine, but no 4 low. It was a wiring issue under the truck. I don't recall what exactly I did, but I know I got a wiring diagram of both the transmission circuit, as well as the 4wd circuit, and once I did that and figured out what made sense going where, it all worked fine.
If I'm not mistaken, there are 3 "sensors" on the t-case computer. A speed sensor, a Clutch sensor, and a neutral safety switch (I'm not sure about the last one, but I think it is). If the truck starts, then the clutch sensor works, it is just a matter of making sure it is connected to the t-case/ t-case computer.
I hope that helps at least a little.
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