the way i imagine my page is that the mainpage is responsible for 90% of the site

sorry but that isn't the way web sites should work. pages should have different urls and you would not really want one url handling 90% of your site content, that would be very bad for search engine optimization.

I mean you could implement that in a custom module using ajax to change the content based on the links, but doing that would have negative impact for search engine placement, I would advise against that idea.

Maybe in your scenario search placement doesn't matter. If you do want to implement it you should not think about it in terms of the mojoportal columns and things that talk to each other across columns, you should make one module that is in the center panel of mojoportal and then inside your module you do the column layout so that all the logic is self contained. ie your module can use the whole width of the page but inside your module you can implement your own column layout for content inside the module.

Hope that helps,

Joe