So a few weeks back I was installing a tail lamp and noticed a couple cracks/holes on my trunk weatherstrip, then checked my spare wheel compartment to discover I've acquired a pool in there.
How do I replace the weatherstrip?

 

I think your better off checking the tail light gasket on both left and right side.
For the weather strip You can simply pull it up, when replacing it align it correctly.

 

My gaskets seem to be fine, I'm going to hose down the car once the new strip is in to double check though

 

When hosing the 'ol gal down, stick a friend with a flashlight in the trunk to check for leaks.

 

And also i agree with checking the gaskets around the tail lights. That is the most common spot for water to leak in.