Unfortunately, we will not be fixing this customized code. The way the app is built now makes it very difficult to script external customizations for BundleBuilder. We've made these changes to comply with Shopify requirements which are meant to improve security and simplify use for all Shopify merchants and customers.
Please remember that most of the customized code was added for our customers as a workaround for existing bugs while we tried to fix those bugs. The vast majority of those bugs are now fixed as part of this new version of BundleBuilder, so those customizations are no longer needed anyway.
We are planning to add a new feature to BundleBuilder in the near future which will make it much easier to add customized code. This feature will be hosted “inside” the app. Doing it this way is cleaner and safer for your store, and also safer for all our other customers.
When that rolls out, we may be able to help with your customization needs again. But we're hoping to make it so easy that you'll be able to do just about everything yourself!