create a custom CodeIgniter app in Expression Engine 2.x

here's some context: our site runs EE 1.7.0 and directs members to our main application, which runs CodeIgniter 1.7.2. We share sessions between the two systems using custom EE extensions and database tables. We want to upgrade to EE 2.x and use the same CI instance. Is this possible or do we need two separate instances? We're considering a "hack" but want to avoid headaches. Our app is too complex to build a module in EE 2.x. Can you advise? Thanks!