Congrats on starting your build---hope to see the progress along the way!
The good news with your van as shown is the rust present is absolutely of no concern at this point.
As you mention rust forming under the OEM mat is a problem especially for those of us in a 4 season climate. Long story short the padding under the rubber portion absorbs moisture over time and it never seems to evaporate out. It quickly becomes saturated and over time the constant exposure to so much moisture the floor will begin to rust. It can go unseen for years, only showing itself when damage is so extensive major body work is required.
As will be seen later my damage was quite a bit more serious.
Having already been through this (and living in Columbus, Ohio too) I used a knotted wire wheel on a robust 4.5" grinder to remove accumulated surface rust. From there I applied POR-15 in the silver color following the instructions to the letter.
Two plus years later there is no sign of any rust re-forming anywhere on the treated areas.
Having learned my lesson with the current E250 EB and seeing the damage done on other vans from those soaked OEM rubber mats I elected to do nothing more than add a 3/4" plywood floor over the POR-15 treated floor. This is by far the most effective method even though some will add layers of various materials in hopes of maximizing sound deadening and heat/cold insulation. IMHO adding layers of this and that do nothing to attenuate road noise and does almost nothing in terms of insulating for temp changes.
As a way to prove this drive the fully empty van on both city streets and the freeway---pay close attention to the sound level coming from the rear. Next place a few sheets of the 3/4" plywood on the rear floor, maybe cut to an approximate shape but only in a single layer---repeat this drive test---the difference should be pretty impressive.
I have a somewhat more detailed write-up on my project for this posted on the FTE boards. For now here is my PhotoBucket album showing parts of my project: http://s184.photobucket.com/user/JWA...Ford/03%20E250
(Pertinent info starts on Page 2 there.)