A big thanks to Toad for helping me out
So after a bit of tinkering, everything seems to work now, with the exception of the large external drives, they will only connect once. I've got 4 different ones, 2x seagate backup plus (1x4TB and 1x2TB) a 1TB Hitachi in a generic USB3 caddy, and an older 3.5" drive in an icy dock powered caddy. All of them will connect once and then when reconnected, do not show up in finder. I have other USB 3 thumb drives that are recognised after replugging.
Does anyone recognise this odd behaviour? Thanks.
Edit: It appears as though the issue is with finder, if I load up disk utility, the drive appears there in a few seconds, maybe 10 seconds, but in IORegistryExplorer explorer, the drive shows pretty much right away, however, in finder and also path finder it takes anything up to a couple of minutes to appear when unplugged and replugged back in the same or other ports, which seems a little odd. Saying that, I can definitely live with this as it is. Thanks again
Edit 2: For some reason, all my external drives are showing as corrupted in disk util with a big red stripe, so I'm repairing those and hopefully that should fix the final issue.
Another edit: It feels now as though there is no graphics acceleration in Mojave now, jerky transitions and generally doesn't feel nice. I just booted into windows and that is very smooth and fluid. I guess this is something else to work out!