I have been working on my girlfriend's 2003 Freightliner Sprinter, and repairing a tremendous about of rust damage throughout the vehicle. The most dangerous area for rust(in my case) was the grommet that holds all the wiring that comes into the fuse panel area under the driver's seat. It was almost completely rusted out. It initially didn't look that bad, but when I removed the seat and seat support to access the area, the grommet metal support(a hole approximately 4" across in the floorboard) completely collapsed and fell away under the van. Please take a moment to look under your van cockpit, and see if you can poke a hole through your floor in this area. It will give you a heads up that this problem is waiting for you in the future.
I mention this because I assumed the completely rusted out driver's side step had something to do with, or was related to the other rust I found in the cockpit. From reviewing this forum, it would appear they are mutually exclusive issues.
I just completely rebuild the driver's side step, and repaired the passenger side step rust damage as well with metal patch panels. To my surprise, we had a little rain last night, and BOTH sides had water(about a tablespoon) pooled in the step at exactly the same place. The plastic steps are both out right now, until we can seal the entire floor with epoxy paint, so there is no mistaking that the water is pooling on the same location on each step, and I believe is coming for a source that is common to each side.
I reviewed this forum, and eliminated the door gasket surround, as there is no water there, or any residual dampness from it wicking down the A pillar and finding it's way to the step. After opening and closing the doors a couple times, I discovered that both doors innermost lower metal edge is INSIDE the rubber door seal, and each door has a rusty hole at exactly the same location as the pool of water in the step, on each side.
Upon closer inspection, I noticed that when open, you can look down the bottom door edge(looking toward the front of the van) and see that the lowest point on the bottom metal of the door is the part that is inside the rubber door seal on the cabin frame. When it rains, or the van is washed. the union of the lower window and the metal piece that separates the window from the triangular shaped fixed window is a natural funnel. Any water that sheds down the glass will fill the trough at the lower edge of the window, at the metal separator first, as it is the lowest point on the window, and keep the edge full until it dumps off the back edge of the window, which is the highest point of the window rubber. A worn window rubber will dump all the water the window sheds INTO the door, and it will then find the lowest point in the door, which is the inner edge of the lower door, and eventually rust through and leak into the driver and passenger door step.
Another tell tale sign that water is pooling on the bottom edge of the window(on this Freightliner) is the rust pinholes that have developed just below the window rubber, which tells me water is being held in the channel that secures the window rubber, and seeking a low point inside the door.
The fix for this, in my opinion, is to open the doors, clean the lower edge of the door panel, and caulk the inside edge of the doors enough so the water, when it enters the lower door, will flow away from the inner edge, and accumulate in the outer front edge of the door, outside the door seal. Then a drain hole can be drilled, and the water will drain outside the cockpit, and can't cause any harm. Of course, if the window outside seal is worn, it should also be replaced to prevent the door from being overwhelmed with water, and flooding into the cab from the top edge of the lower door metal.
I hope this helps.