To put this to rest - the transfer did not go as smoothly as we would have liked. I count myself lucky to have brought the template as far back from the beyond as I did, and to have recovered as much data as I did. I have no idea why the design is not behaving correctly (such as the changed tree links at the top and the loss of the link at the bottom).
My plan going forward, time permitting, is to do a full version upgrade to SMF 2.0.1 which will doubtless ruin our layout anyway. So this is a transitional version anyway - we'll probably be looking at a whole new look in a matter of weeks.