Customisable embedded processors that are available on the market make it possible for designers to speed up execution of applications by using Application-specific Functional Units (AFUs), implementing Instruction-Set Extensions (ISEs). Furthermore, techniques for automatic ISE identification have been improving many algorithms have been proposed for choosing, given the application's source code, the best ISEs under various constraints. Read and write ports between the AFUs and the processor register file are an expensive asset, fixed in the micro-architecture - some processors indeed only allow two read ports and one write port - and yet, on the other hand, a large availability of inputs and outputs to and from the AFUs exposes high speedup. Here we present a solution to the limitation of actual register file ports by serialising register file access and therefore addressing multi-cycle read and write. It does so in an innovative way for two reasons: (1) it exploits and brings forward the progress in ISE identification under constraint, and (2) it combines register file access serialisation with pipelining in order to obtain the best global solution. Our method consists of scheduling graphs - corresponding to ISEs - under input/ output constraint