 Re: the use of the past perfect tense
First of all you don't use past perfect to say that something happened or that someone said somethng long time ago. You use it to place /locate some events in time in reference to other events. That is, you highlight in this way what happened first and what happened next.
Also, you have given two different sentences, they haven't much to do with each other:
1)The media said that the boys weren't involved... but the original sentence was: '(The media say) the boys are(present) not involved', then you added 'The media said(past)' which implies a change in the tense, from present simple to past simple, just because the introductory word 'said' determines such a change.
2)The media said that the boys hadn`t been involved... but the original sentence was: '(the media say) the boys weren't involved', you, again, added 'The media said' which, again, implies a change in the tense.
Look at these examples:
1) Szymon says(present tense) that Robert is (present tense) nice-the original sentence.
But if someone wants to tell someone else what Szymon said about Robert it will be like this:
'Szymon said (past simple) that Robert was (past simple) nice.
so the pattern is: original sentence (present tense - present tense) and Szymon's rephrased sentence: past tense - past tense, notice the consistency in the change in tenses.
2)Szymon says (present) that Robert was (past) nice.-original sentence
the pattern here is: present-past (different tenses)
Now, after someone else said what Szymon said about Robert:
Szymon said (past) that Robert had been (past past, so to speak, in other words-past perfect)nice.-rephrased sentence
So, the consistency is the same but there is one tense level difference, is that clear?  | 
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