Taking on water in the interior

I have a 74 swinger, just finished welding new floors in. I seam sealed the welds and the next day it rained hard. When I got home and opened the door, there was standing milky fluid where the low spots of the floor are. Water got in and washed some of the sealer out before it could cure. I already knew water comes in and culminates on the rocker panels, but this is a lot more leaky spots than I thought. The worst I think is right under the heater box. In the passenger side floor in the right front corner, where the firewall comes down. I've been trying to figure out where the water could be coming from. The windshield weatherstriping is going to be replaced with the windshield but I don't think it's that. Could it be something in the cowl?

All the other places I think are leaking from the roof rail weatherstriping (both sides) that looks worn out. I will be painting the floor with truck bed liner so it shouldn't make the floor rust out again but I don't want the carpet and seats to mildew from water coming in and sitting.

Also where the trim is supposed to go on the windshield was filled with bondo by the previous owner and the places I've peeled up are rusty and chipping off. My friend said I should take the windshield out my self so I can remove the rust and re paint it before the new windshield is put in. Do you think the rust will affect the new windshield? I don't even know how much it would cost to fix that if it's too bad, so I'm hesitant to even touch it right now. He also said there might be holes where it's rusty in there, letting water through. Could this be my problem? Thanks in advanced.
Dom