@Addicting I'm sure you've been researching this, but the 99s had some quirks. First year for the chip in the key and security system that had problems. You can program it out when you do the ls swap. Also, check and see if the brakes got the service bulletin addressed for the rear brakes. It required a new proportioning valve you can't get anymore and they all look exactly the same, thanks GM.
I had a 99 sub 2500 similar to that and got real deep into some of the bizarre electrical on mine. Sold it a year ago.
I already want another one to ls swap thanks to your post. A 94 2500 with 147k on it for 3,000 has been tempting me lately.
Good luck with the project! Are you still going to swap in the 6 speed or leave the 4l80 in it?