Following the comments on here I concluded that it must be a fuel problem. On Tuesday I went down to the boat with the intention of checking every bit of the fuel system that I could, to hopefully reveal a problem. I worked from the tank, back, checking all the hoses, connections, breather etc etc. I eventually got to the engine, checked the internal filters (yes there are two - I discovered anther small one). I then got to this "thing" which (you can tell I'm not a mechanic) I think is the pump (see photo). Anyway, I noticed that whatever it is has a drain valve on the bottom, with a small hose coming off it, as well as a breather screw on the top. I assumed that this must be to drain the fuel off, so I gave it a go. It did indeed drain the fuel out, but what was most interesting was that when I drain it out there were some bits of debris in the fuel. I flushed fuel through it and then out several times, then blow back up the hose, followed by more flushing and more blowing.
We have used the boat a few times since, just running around the harbour, and so far it seems fine. I did take it for a short test run at speed, where again it was fine. I'm hoping and praying that this was the problem as it seems to be a nice quick fix should it happen again. The proof will be this weekend when we take the boat to Weymouth for the BUSA Nationals.
What I find odd though is that debris managed to find it's way in there. The trouble originally started around the same time that the main transom mounted filter/separator got damaged, so we bypassed it for a week or so until I got a new one. That would still have left the two internal filters, neither of which had anything significant in. Any thoughts?