The trans controller will be the trickiest part. Standalone after market ones are pretty expensive (~$750). Since you also need to deal with merging the accessories, I think the easiest way to do the swap would be to harvest the wiring harness/computer and accessory brackets and pulleys from a junked 92-93 GM diesel since most of those (I think) have the controller for the 4l80E but used mechanical pumps like your 6.2. This also has the best potential for being able to use as much of your 99 accessories as possible.
I looked at going this route for my 93 454 conversion, but ended up just getting all of the parts for a 94 6.5TD since I didn't already have the 6.2 like you. I still like the idea of using the 6.2 for the milage potential, though.
1993 GMC Suburban K2500 currently 7.4l but building 6.5l turbo to drop in with harnesses/computer from 1994 C3500 donor