Water - from various sources - is expected to enter the fresh air inlet plenum along with the fresh air. After passing through the wiper cowling and leaf screen, the water is then shed to the left and right within the plenum:
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When it reaches the outer ends of the cross ducting, it flows into the down flow trunks on either side of the cab:
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The air is allowed to enter the cab through the vents in the kick plates and the ventilation fan suction. But the entrained water can't make that turn, so it just continues straight down to the bottom of the plenum. At the bottom of the trunks, there are openings to allow the water to drain out on to the ground:
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But that is only always the case in a perfect world. In reality, things are different. After 30 years of debris being sucked in (and mice living in the duct work, rust flakes falling down the plenum, etc), those drain openings can become obstructed.
If it gets bad enough, the water can't flow out as fast as it comes in. Eventually a level of water develops in the lower section of the down trunk. If it gets high enough, it will begin to flow out over the lower lip of the intake vent. From there it seeps down behind the kick plate panels and puddles up on the floor pans:
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The scenario described above is the most common cause of standing water in the cab. As long as you don't have any huge gaping rust holes in the cross plenum, roof or any other horizontal surface - it is most likely why you are getting water in the cab.
To find out for sure if that is how the water is getting in, do a wet test. On the windshield, set up a garden hose - running full blast. Direct the water so that it can enter through the wiper cowling and down into the cross plenum. Even at full flow, the drain openings are big enough to handle the quantity of water coming out from a hose (if they are clear).
Then, with the water from the hose flowing into the fresh air intake system, walk around and look up between the fenders and doors. You should see plenty of water gushing out on to the ground. But even if that is the case, don't trust that the drains are fully clear. Continue to run the hose to see if a level is forming and slowly rising. After the water has been running for a while, open the fresh air inlet vent doors and see if any water is coming in. The volume of the down trunks is pretty big so it could take a while for the level to rise high enough to spill into the cab. I'm sure you'll figure it out.
