Fastforward,
Sorry for the delay in replying, I (quite stupidly) did the upgrade quite late in the evening and when I encountered the problems just killed the whole process and re-started it again this morning...
Anyway...
I was running 2.4 for B3, but I downloaded the 2.5 and 2.6 versions of the usenet hack and applied each SQL upgrade instructions seperately - so as if I had upgraded to 2.5 then 2.6...
I checked the usenet_article table and found over 3000 articles in there...since this is a beta test for my users I decided to empty that table and all other tables apart from the tables that seem to have settings in them.
I re-ran the script on the one newsgroup (that I know only has a few hundred posts in anyway) and the whole thing went really quickly...i'm doing some more testing and starting to re-populate the forums now so will post more details on how I get on later...