By the way it always helps to give at least a little bit of info like what year your truck is, other mods, etc. I had to browse through your older posts to see that you're installing this in an '89 and you already know you need a standalone controller to operate it.
That transmission is a mid-'97-up as evidenced by the separate bellhousing. Earlier ones look more like your old 700R4 with the bellhousing/case as one piece.
From '95-up they have a range switch (or neutral safety switch, if you please) that fits over the shift stud, that's why the stud is longer than earlier transmissions. Its primary function is just like the one at the bottom of your older style column; it prevents starting unless in park or neutral, and also provides the reverse light switch. The other function the '95-up switch provides is the input to the gear indicator LED's in the dash cluster.
'95-up shifting is done by cable, but there shouldn't be anything stopping you from connecting your older style rod linkage to it providing you can make the bracket for it fit the stud. Might even be able to swap the stud out for one from the older type transmission. Wouldn't know; haven't tried.
Richard