2000 996 will not shift into 1st, 3rd, 5th, or reverse
 

I have a 2000 996 with 123,000 miles on it and this morning it would not shift into half of the gears. I was able to get home starting out in 2nd and shifting directly to 4th. But 1st, 3rd, 5th, and reverse the gears would not engage. No power was applied to the wheels. Does any one have any experience with a fault like this? Also looking at parts on Pelican the shift lever attaches to a blue cable and a black cable, what is the difference between the two?

Check linkage. Read manual.

If it's not the linkage it's a transmission problem. Hopefully you just lost a cable. I'm runnying a tiptronic but I think manuals use cables. So hopefully it's just a disconnect you need to resecure with a bolt.

Check your cables, one has either popped off or snapped. Not super common, but does happen. Check this link:
! Stuck in 3rd, Shifter Feels Disconnected, Cannot move Left-Right or Change Gear - Rennlist Discussion Forums

I got the center console apart and both cables are connected. Also checked the cables at the transmission and they looked to operate fine! Anyone have much experience with the 996 (G96) transmissions? Is it better too troubleshoot the problem in the transmission or replace with a rebuilt?

Were there any symptoms leading up to the problem? I don't think any of the internal shafts and gears of the transmission are going to go out with out you knowing it's going to happen.

Looking in the manual I'd think the support bracket sleeves is where you might be having a problem. The bulky parts of the cable that hold the insulation around the actual cable that moves have to be fastened down for the cables to operate the trans. Both cables top and bottom have to be fastened. Check and make sure they are engaged. The manual says you must hear and feel them engage which I figures mean they snap in.

There are adjusters just forward of the stick before the top side braket sleeves. It looks like you trist the adjusters open.