This is probably not what you are looking for, but you might consider using naturally occurring linkers. One great example of that is the linkers in modular polyketide assembly lines that catalyze the synthesis of natural products. These are multienzyme complexes, comprising several modules, each one catalyzing the extension of a polyketide chain with two carbon units. These modules are either encoded onto one open reading frame, or several modules are encoded by one ORF. There are linker regions between each module-module pair, as some linkers are intra-peptide, and others- interpeptide. Both types of linkers have been successfully used in engineering hybrid module-module pairs, in which these linkers will facilitate the protein-protein interactions between the hybrid module-module interfaces (ref). Unfortunately, I don't know of an example of using these linkers for fusing other than polyketide genes. But I think it is worth looking into it.