Tons of condensation in 2000 Mk IV trunk

My 2000 Jetta TDI has had a lot of condensation in the spare tire storage area. I haven't found any drain plugs missing, etc. Does this sound like a skylight drain that is plugged up?

Sounds more like leaking seals around the tail lights. Sunroof drains leaking will leak into the cabin area not the truck IIRC.

In the Jetta (sedan anyway) sunroof drains drop out of the bottom rear "under" the trunk.
Is your trunk carpet wet? Where exactly? Have you removed everything and I mean everything from the trunk (spare and etc.) and checked for holes in the floor of it?

Ecs sells the tail light seals or you can search Google for best price. Part number is 1J5945191.

Could be roof drains, a bad seal (my '99 was bad when new) or tail lights.

Definitely check rear sunroof drains - I had one of the two rear ones block up on my Jetta some years back, and it sent a bunch of water into the spare tire well.