Note: You mention it (the 003 tranny) shifts on vacuum and has interior clutch. Are you talking about the 3-speed auto stick shift tranny that come in the VW Beetles? If so, there's not much you can do with one of those transmissions. It is the only VW transmission that I am aware of that has both a torque converter and clutch. If so, it would never handle the torque of an ALH engine.
As for programming, since the 003 operates on hydraulic pressure for shifting purposes, programming would not be necessary and there's nothing to program (electronically speaking in the older models). There are a few automatic Vanagons with TDI engine installs (check the Sticky for Vans) There are a few that have the aftermarket Ring and Pinion (seems it is 3.27:1 ratio) for about $1,500.00 plus installation[vendor in California with product from the UK]).
The 003 transmission (technically 003-010) is basically the same as the 010 that come in the older gasser Jettas, Rabbits and Golfs (the end with all the gearing will bolt up to the diff of the 003-010) going back to about 1972. It is a 3-speed
without a lock-up torque converter and has a low geared Ring and Pinion (something like 4:1), which is not good (you don't want a high-revving TDI in a Bus). I have no clue how an 003 could be "turned into" a manual 4-speed. Seems it would be best to just remove it and install a regular 4-speed! Of course, you will need the shifter, shifter box, and shifter linkage.
There are a few Bay-bus TDI installs documented here in the TDI Conversions category. They should have helpful info.
Lastly, the electronic aspect of the ALH conversion is a challenge in of itself..
Here is a link to an 003 being rebuilt:
http://www.thesamba.com/vw/forum/viewtopic.php?t=570692
Here is a link to the aftermarket Ring & Pinion:
http://www.thesamba.com/vw/forum/viewtopic.php?t=431013&highlight=
Here is a link TDI bolted to an Automatic:
http://www.thesamba.com/vw/forum/viewtopic.php?t=271437&highlight=