An approach that might work would be to run the module stripped of all encounters, referencing a second encounter booklet that is designed for the specific system, be it 4e, Pathfinder, or whatever. Then sell the PDF with each system encounter book at a fixed price that will attract customers, but also offer it at a marked up price (or bargain price) that includes the other systems. The print version should be sold so that it includes all systems to reduce printing costs or done POD as suggested (however this limits FLGS sales).
As for design of the encounter book, I would try to focus each encounter so that they cover a one or two page spread for easier referencing, cutting out page turning. The arrangement would be similar to late 3e and current 4e encounters. I personally don’t think it will work, but if it is going to work then layout will be the key to its success and survivability.