YF...install johnni bolts back through the red flange and resecure the red flange exactly as it was. It is a repair flange and looks like hubby did a BANG UP JOB in terms of the approach to the issue (he could have just tried to CAULK the toilet to floor)!! Sorry! I really wanted to slam the guy for ya!!
Then set new wax gasket and re-set the toilet...That should be all you need to do. By what I see...there is no reason for toilet to rock if red flange installed properly.
If rocks after re-installing..get back to me ASAP..I am flying to Lake Isabella!!
Mark
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