I feel for you cos you've clearly put a lot of effort into this.
I could only think to try make the bonus links clearer: https://www.warlight.net/SinglePlayer?PreviewMap=50032
For some reason Warlight's distorting the bonus link objects a little; the numbers are perfectly clear in the SVG: http://imgur.com/C6szf92
Whilst this might be a temporary solution, I think the main problem is going to be that territories are too small; they're barely squeezing in a 2 digit army: http://imgur.com/ivyZanO
A map this size will easily accumulate stacks of 100+, eventually 1000+ and then it will not be very clear to distinguish the army totals in a territory when these numbers all overlap.
What this map truly needs is for the canvas size limit on warlight to be increased. I think it's called page size in inkscape. If your entire map could be scaled up, the bonus links could all be normal sized, and thus fit nicely, and the army numbers would also shrink to fit. I'm not sure why this 3330x2400px page size limit exists in warlight--I thought SVG's vector graphics meant it can be scaled without affecting file size. I'm sure there is probably a reason for it, (though I don't know it) and as long as that limit exists, it's sad to say it but I just don't see a way.
EDIT: Check out the Caribbean when you preview the map to see what I mean.
Edited 11/27/2015 23:32:28