All pre-2000 TDIs in North America are not OBD2-flashable. That means you cannot use OBD2 flash tools like FlashZilla.
They require ECU (engine computer) removal and physical chip swapping. Surface-mount soldering is also required in order to install chip sockets, especially in 1999.5 Golf, 1999.5 Jetta, and 1998-1999 New Beetle ALH TDIs. We also offer ECU hot swap services, as long as we have matching ECUs in stock. Click here for more information including pictures.
Click the following link to see a picture showing where to put "H" and "L" chips (we already do this for you, if using our socketing service):
Are you installing a 1998-1999.5 ALH TDI ECU with a part number that's different than your original? You may have to grind off small plastic tabs on the ECU to make the it fit: Click here to see pictures.