I managed to UV the dynamesh model with Zbrush's UV master and took it into Mudbox to paint up the textures more thoroughly.
Mudbox's texture layers were way faster and easier to work with than Zbrush's poly paint. And I could make other material channels. Wish there was an easy way to duplicate a whole layer stack though. Duplicating them all and setting up the masks again was a pain. Especially as I encountered a bug preventing me reloading the scene after I'd duplicated all the texture layers and had to do it all again. Good job the textures saved ok so I could just load them up on an older file.