Take them off in any sensible order - but always slacken the rocker shaft nuts (1/2" AF) before slackening the head nuts (9/16"AF) to avoid the poor wee rocker studs having to carry the full force of the valve springs - reverse is true when refitting. When tightening - first do them all up 'slack' - then start tightening with the front centre nut (standing at the UK driver side wing - looking at the engine sideways) and then alternate outwards to left and right front to back slowly tightening each nut a little as you go - back to centre front and continue round and round. Initially tighten to 30 ft.lbsf all round - then go up to 35 then 40 and finally 44 on the last round. Then set the valve gaps 12 thou inlets and 15 thou exhausts.
did you just yank the rods out or pull them out carefully? If the former there is a high probability that you have dislodged the cam followers. If you think that might be the case, you can remove the little rectangular plates on the side of the engine (unless its a 1275) to put them back
Yep - pushrods must be shaken, not stirred to make sure the followers are left behind. And believe me - with 15 thou exhaust valve clearances you are FAR less likely to suffer burned valves!
You won't break a stud at that figure - the gaskets now don't contain asbestos - the higher figure gives better clamping. Later cars have 'dimpled' studs (we used to covet these for our rally cars 35 years ago!) and can be taken up even further - and finally the A+ Minis have 'Y' stamped on the ends of the studs and can go safely to 50 ftlbsf - and even more with some risk. All these of course still have the same anchor arrangement in the block - which is interesting. I have never snapped a stud or pulled one out the block - but I have stripped the upper (fine) thread a couple of times when using worn nuts. Always best to check your nuts.
They should NEVER break at 40 !! Either very poor stud - or it had been seriously overtightened in the past - or something wrong with torque wrench. On that basis - the nuts shouldn't even be tightened to 40 ftlbsf - which would be hopeless.
And naturally you can tell that in advance, and happily tighten them however much you like. Very little point arguing about this - in my opinion, the figure given in the workshop manual is the one to go for. Others may disagree, so it's best to know the dangers.