This paper presents a novel framework to generating efficient custom instructions for common configurable processors with limited numbers of I/O ports in the register files and fixed-length instruction formats, such as RISCs. Unlike previous approaches which generate a single custom instruction from each subgraph, our approach generates a sequence of multiple custom instructions from each subgraph by applying high-level synthesis techniques such as scheduling and binding to the subgraphs. Because of this feature, our approach can provide both of the following two advantages simultaneously: (1) generation of effective custom instructions from Multiple Inputs Multiple Outputs (MIMO) subgraphs without any change in the configurable processor hardware and the instruction format, and (2) resource sharing among custom instructions. We performed synthesis, placement and routing of the automatically generated Custom Functional Units (CFUs) on an FPGA. Experimental results showed that our approach could generate custom instructions with significant speedups of 28% on average compared to a state-of-the-art framework of custom instruction generation for configurable processors with limited numbers of I/O ports in the register file and fixed-length instruction formats.