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. You will be responsible for ECU socketing. 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.