The transmission pan gasket takes about 1.2 hour to replace. There are several 4 cylinder engines and several automatic transmission applications in the1999 Jetta (diesel and gasoline). One transmission calls for special long life transmission oil the other calls for regular Dexron oil. Make sure the shop repairing the leak are experienced in "newer VW's".
When I have done them, it has been pretty expensive. It is about an hour of labor, but the expensive part is the factory approved fluid. I have billed out from $200-300 for this job if I also change the filter. the filter and pan gasket kit runs about $51. Good Luck!