no one had certified the COMBINATION of all the mods as one package.
A common worry. What is supposed to happen is that the STC should be qualified as to serials applicable and compatible mods. Certainly, those of my origination in the past had words to keep things clean. This is also a responsibility of the installing agency to make sure that things are not incompatible.
The cited problem ought not to arise but, of course, it does.
This is precisely what I was told
There is plenty of information available which is useful for background and general knowledge. However, the main aim should be to remain within the AFM/POH authorised envelope and operate with a bit of commonsense. I can recall one minor battle I had in respect of operation at higher thrust. The AFM said "at pilot discretion" but didn't bother to say explicitly that this meant OEI. The operator's boss decided that the words applied across the board and I lost the argument because of the contract words.