I bent mine back into shape (open about 1/8"), painted over w/ the POR & then covered all w/ the protecto wrap & then went back & cut the triangle out of the protecto wrap so it will drain as factory
I don't know for sure what you should do, but after inspecting my car I've determined the floor pans must have rusted from the inside as the entire bottom is coated with a sealant of sorts. also the carpet is still a tad wet(i got it in my garage Monday). So I'd consider not plugging them.
I just ordered the POR 15 kit and I'm looking at options for carpet as well as using roofing material with insulation on one side and the aluminum on the other then then possibly outdoor carpet. The floor would be POR 15, Quick roof peal and seal, then possibly indoor outdoor carpet. I've been debating this seal the hole up question for a couple weeks as I figure out exactly what i'm going to do. It seems to me there are two issues.
1. trapped moisture would creat rust.
2. trapped moisture would create mold.
if you are using any type of jute pad i would say leave the V cut in the floor. POR 15 is designed to resist moisture, so if you are using POR 15 and not using Jute or cloth pad i would not be too concerned with sealing everything up. if you seal everything up and get caught in the rain you may want to take additional steps to dry the car out such as leaving the top down for a few days.
Personally, I'm still not sure and welcome any thoughts on this as well.
cool heres some thoughts
clean it all up cover it well with por15 and dynamat or a open cell foam pad"or both"
open the vents if you seal them in at first
cut a hole around them 1 inch or so
the foam padding and auto carpet from the box store
then keep it dry
thats the plan anyway
also use a heat gun when applying dynamat or simalar products