Very well done , Fred ; sounds like you are on the home straight now
You are right about those tiny collets , the only way I could handle them was by hanging them off the end of a magnetic screwdriver . And I dropped them a lot !
Re the thermostat , on balance I would personally renew it whilst it is exposed . But there are two schools of thought here . One says do it all whilst you are in there and avoid having to go back for a long time, and the other says if it ain't broke don't fix it and that the new parts will be rubbish quality compared to the old ones and won't last as long anyway
Sounds like you'll never know just what went wrong and when , but your theory about a past bodged job sounds fair enough to me
Out of interest , you mentioned varying loose head bolts ; was the head you have taken off flat or might it have been distorted ?