A system, including methods, apparatus and kits for connecting bones and/or bone portions using a multi-part bone connector with one or more rotating joints is disclosed. A flexible bone fusion apparatus is provided having an anchor and a compressor, each of which engages with a coupler to provide axial and/or linear rotation of the apparatus. Alternatively, a compressor and an anchor may directly join with each other at a shared interface. Tools for installing and compressing the apparatus are provided. Also provided is a method for fusing two bones or bone portions to create a non-linear post-fusion orientation. A further aspect of the disclosure is a method for maintaining thread synchronization of a bone fusion apparatus having a discontinuous thread.