I wasn't particularly happy with the stock shift lever, so I bought one of the short shifters. I was also dissatisfied with it; mainly because of the odd angle, but it also felt a little too notchy. I also wanted to replace the old knob, but both levers being flat meant I would have to use one of the clunky knobs made to fit.
So, I decided to make a new round shift lever that would allow the use of a normal threaded knob. The factory lever has about 1 inch of round before the metal is flattened so the knob slots on. I cut the flat portion off and threaded the remaining round. I then took some stainless and turned a new lever on my lathe. One end is tapped with 1/2-20 threads and is loc-tited onto the shortened shifter. The other end has a male thread that fits common 1/2-20 knobs. I had some walnut, maple, and brass, so I also made a 917-style knob. The old knob was cut from the leather boot and I made an aluminum collar that slips over the new lever.
I think it turned out well.
If you don't have a lathe, I think you could get similar results with off the shelf parts from McMaster Carr or the like. eBay has shift knobs of various colors and in various thread pitches with the right shift pattern for a 996. And you could make a shorter shift lever if you wanted, though mine is stock length.