Ok, so having spent quite a bit of time on this, I would have to downgrade my assessment to semi-successful - ha! I ended up having to install alot of emulators that I thought would still be on there as they were on my old build, and nearly all the other emulators had binary updates for me to run.
My RetroPie build is very basic really, with the only tweaks being those detailed in the official docs, so looking back I think if I was to do this process again, I would just start completely clean and go through each system one by one to check all is working correctly and updating/tweaking as appropriate. At least then I would know what needed to be done, rather than finding some things had copied over and other bits hadn't. This is most definitely due to errors on my part I'm sure.
On the plus side, on my 4.4 build my Sega CD and ZX Spectrum games wouldn't work (Sega CD would jump back to ES, and ZX Spectrum would crash the Pi) but now they do, so not sure what happened there but it's all good now - ha!