I've recently been working on restoring a car that had been sitting around for awhile and have come across this issue where the trunk begins to flood when it starts raining, I don't have much to say beyond that but I do have pictures of the trunk and where I think it is coming from.

 

That looks like it's coming from the seam that seals the rear glass to the rear panel.Your sealant might be dried up.

 

Ok, i'll see if thats the problem, I'm going to try to pull the panel and trunk strut off to look into it further, thanks for the advice.

 

Knock the body plug out of the storage well and let that water drain.

Check around the flat black plastic filler pieces that span the gap between the glass and decklid. The plastic filler is supposed to be sealed to both parts with the gap filled.

There's also a ton of seam sealer where the 1/4 panels meet the tail panel. You'll see the seam just above the tail lights on either side. The bulk of the seam is behind the tail lights. If the sealer is dried and cracked, the rain water will just run down the gap and enter the trunk.

 

Well I think I've narrowed it down to a passenger side area issue as when the panel was piled ofc this is what I got. Passenger side
Weatherstripping possibly indented?
Driver side, rust stops about midway.