Hi @sethregan, at the moment, combining the sites after export, using the first site exported as the main site to merge files into, is probably the best solution until the page limits in Webflow on a per site basis are increased.
I tested the export scenario with a couple of exported sites, using symbols with relative path links, and after merging the sites (after export), the site appears to work as intended for me.
I know this is a hassle and I wish I could give you an ETA for when page limits will be increased. As soon as there is a change for this, it will be updated on the Wish List here: http://forum.webflow.com/t/increase-page-limits-on-individual-and-team-plans/4981
Let me know in case of any questions, I am here to help.