When a large project hits limits

I have a large feature-rich site (I'll call it site 1) that can't handle adding more functionality to it. However I need to find a way to allow 1 type of group on site 1 to have separate instances of ubercart i.e. most members in that group would have a store. approx 200.

I would need the 2 sites to be connected. The admin of the group on site 1 would become the owner of a store on site 2. Users on site 1 can buy on site 2. There would be a few shared tables for roles, content profiles and group node data and members.

Site 2 could be set up with it's own Drupal core, Domain Access for the multiple stores, Domain Ubercart and Ubercart. (As well as shipping, theme, etc)

Is this possible? I can't find anything on how 2 sites with separate code bases can be connected somehow. It's just not possible to add more modules to the main site.

Just in case someone suggests it, Ubercart Marketplace doesn't allow for flexible shipping so it's out of the question.

I believe this is for a very important cause so I need to find a solution. This is more of an 'application' than a normal website. The main site is for environmental participation with 3 dashboards for all kinds of activities for 1. Individuals 2. environmental non-profits and 3. all other organizations. The stores become a way not only for the environmental organizations to receive donations but also a new way for them to make money and promote local 'green' products. This is a very innovative site that goes beyond just what I've mentioned here but right now I'm feeling like I'm carrying the weight of the world on my shoulders doing this by myself. I'm in the home stretch. I need just this last part and I'd be so grateful if someone can tell me how to do this.