Sometimes something as simple as a poor ground connection at the area under the battery can cause seemingly constant or bizarre problems. If you are so inclined clean and secure every connection particularly ground connections ( usually solid brown color wires ) you can get at under the hood , particularly at and under the battery. I have resolved many ongoing stories like yours this way. An additional thought would be to make sure any accessible electrical connectors are clean and tight !
Ask a mechanic to check your Ignition Module. My Beetle's turn signal was getting stuck.. click click stuck, when it was cold or when i hit a hard bump. About 2 weeks ago, they stopped working all together, but the hazard lights still worked. The headlights wouldn't come on, but the hazards still worked and the dash lights worked. New Ignition Module, poof, everything works! Good luck!
My father told me, AFTER I bought my 2000 Beetle, that the wiring in beetles between 1999 to 2003 or so all were outsourced and the company was really shaudy. Expect more problems.