I managed to work through the list from the structural engineer over the last few days and tick off every item from his list.
The first was to remove a section of the wall plate as the cantilevered section was rotten (the bit sticking out past the wall). This wasn't as awkward as I thought it might be, just a few 6 inch cut nails to contend with. I half lapped the new section of wall plate on, which I planed down to size as it wasn't standard, and added the strap across the top to meet the requirements the engineer had set.
This picture shows quite well why I think the roof should have been replaced- the rafters are cut on to the wrong side of the wall plate creating pressures and forces in the wrong place so its pushing out not down. I know the purlins reduces the load but I just don't like to see work left thats not right!
The next step was to splice the barge board on the end where it had gone rotten, as well as add a new cocking fillet.
I then had to add 450mm new ends to the rafters which had the worst levels of decay.
The worst job was to then chisel a section of wall plate around 4m long and add a ply facing. This was to straighten it up and provide a fixing for the gutting. This job did my chisels no favours as it was full of nails.
I also added a ply soffit to both ends and fitted the a complete new gable ladder with barge board on the far side (not an easy job on your own!).
When I'd finished I couldn't help but add a fineal to both ends just to finish it off (I wont get paid for that bit but I don't care!).