fizzbizz, your OP sounds like one of mine a while back, right down to boy crying wolf I started the thread in the parenting section some time ago ( last post was in February). Thread was called 'My 12 year old son is ill such a lot - low pain threshold, attention seeking, serious health problem, or just bad luck?' I MUST learn how to do links!!
Anyway, very much the same problems as you but things seem to be on the up. In the autumn term of Year 8, my son was off sick for about 20 school days, though admittedly 12 of those were due to mumps (diagnosed by GP). In the spring term he was off school for two half days - docs appointments - and 2 full days, over the whole term, so much more respectable. So far this term he has been off for 1 day.
I reached a low point when on the VERY FIRST DAY of the spring term, ds announced he had an earache, after feeling perfectly well for the two week christmas holiday. OK he has ear problems but it's amazing how they tended to only happen during school days.
Anyway I digress. What I did at the beginning of the spring term was get the GP to have a serious talk to my son about keeping going if pain is slight, now he is 13 years old - not expecting to feel 100% fresh and alert and totally pain free before he can go to school.
I also promised to give my son calpol meltlets to take to school every day. Any pain and he was to take a meltlet and wait for half and hour so it took effect. Only then was he allowed to go to the sick room and ask to be collected.
If he woke up in pain I would expectd him to take pain killers first, then wait to see the effect. Again only if painkillers had no effect could he stay off school.
If he woke up feeling tired or sick, I would be pretty determined in getting him to go to school, saying I would collect him later if he was still ill.
If he really resisted that, and I suspected he might be a bit out of sorts, I'd wait at home with him for an hour or two to see if he still felt bad. If he was seeming to recover, he would go into school late. Sometimes a later start in the morning was all that was required. Not ideal but better to miss the first two lessons of the day than all eight of them. And IME it is harder to keep up any pretence of being sick if you have to do it in front of your mum for a good few hours.
I also said (and I know I may get slated for this by MB)ds and I agreed that he was allowed two 'rest and relaxation' days a term as long as he took little or no time off for being sick.
These were days when he could catch up with sleep - no questions asked. My son does quite a lot of extracurricular stuff ( sports and drama at local theatre) and sometimes things can get really busy for him.
There was a three week period towards the end of last term when he was reheasing a play all day sats and sundays, doing 2 or 3 long evening rehearsals and still doing all the school stuff. He didn't miss any days at school but held on to the promise of two rest days which he chose to take on a Thursday and Friday when the play opened.
Ds seems a lot better about going to school regularly. He does still get grumpy some mornings but is careful to not 'squander' his two R&R days for this term.
He also admits that things are much better if he is at school most of the time - he now sees how easy it is to get out of the swing of things, miss out socially and get confused about what homework he has, just by missing lots of days here and there.