Two options;
One - Normally I would create a new field in collection 1, make it multi-reference linked to collection 2. Using the text field as your pointer (your unconnected join field), manually set the value to the correct collection 2 record. Now they are linked.
Two - Use the API to set the multi-reference join. This would require developer skills and a knowledge of the API.
Since I can’t see your project, that is as specific as I can get.