HARMONI is the first light visible and near-IR integral field spectrograph for the ELT. It covers a large spectral range from 450nm to 2450nm with resolving powers from 3500 to 18000 and spatial sampling from 60mas to 4mas. It can operate in two Adaptive Optics (AO) modes - SCAO (including a High Contrast capability) and LTAO - or with NOAO. The project is preparing for Final Design Reviews. The SCAO system for HARMONI is based on a pyramid wavefront sensor (PWFS) operating in the visible (700 – 1000 nm). Previous implementations on very large telescopes have demonstrated the challenges associated with optimising PWFS performance on-sky, particularly when operated at visible wavelengths. ELT operation will pose further challenges for AO systems, particularly related to the segmentation of the telescope and the control of badly seen ‘petal modes’. In this paper we investigate these challenges in the context of the HARMONI SCAO system. We present the results of end-to-end simulations of our baseline approach, using a coupled control basis to avoid the runaway development of petal modes in the control loop. The impact of key parameters are investigated and methods for optical gain compensation and optimisation of the control basis are presented. We discuss recent updates to the control algorithms and demonstrate the possibility of improving performance using a form of super resolution. Finally, we report on the expected performance across a range of conditions.