I was looking over the pictures after I posted them and had to pop back out to the garage. The top of the rear brake arm has been bent in towards the wheel. Rub marks on the rod, exhaust bracket and shock show it was ridden this way for a while and then someone tried to fix it by routing the rod on the outside of the exhaust bracket and bending round and back inwards to meet the bent brake arm. I managed to tweak the brake arm straight and with the rod roughly straightened out it will now run along inside the exhaust bracket and meet the brake arm without fouling the shock. The old rod is still scrap so I'll finish up the new one tomorrow and I guess I will have to road test the bike again.