Hi,
As I see you are putting much time in these things (I have your mails but it will be some days before I get to them), I will answer before processing all the forum

jumplinks are used for a variety of things, they are links between 2 regions, not necessarly adjacents, and give a specific cost between these 2 regions. So you can use them to show the crossing of a river, to prevent a ship from moving to a particular sea (harbor exit point), to prevent a troop from passing from region A to B (a high mountain peak) and such. So yes this is normal to have such links between regions which are not separated by a river (you can even use them as teleporters).
For more details, you should download the AACW database, there is a file called terrains.xls where jumplinks are listed, you will understand better. If you want to review the links between each region, then we can send your our map utility, this will be more handy for you.