Four days later, so I don't know whether you are still working on the Guardian Genius puzzle, Shivster. I did finally have a chance to look at it and what must have happened earlier to my copy was that I got a few answers on first looking through them but then put it aside. Thereafter, it got lost, as I suggested.
However, I have now had a chance to complete it and I think I've - sort of - got the answer as to how the grid must be completed.
As you know, there are certain letter-clashes, such as the 'O' in 1 D with the 'G' in 9A. I have found 13 of these. Now, there are 14 letters in the words 'GUARDIAN GENIUS' and the clashing pairs I've found are G/O, U/A, A/E, R/D, D/I, ?/?, A/E, N/O...G/S, E/I, N/I, I/E, U/N, S/L. If you look at the opening letters of these, you'll see that they spell 'GUARD?AN GENIUS. Sadly, I can't find the missing 'I'! (Other ways of selecting the sequence also exist, of course, so maybe it's not an 'I'.)
My assumption, therefore, is that the 1D/9A slot, for example, should contain the 'G' and not the 'O', because there is no 'O' in the two words I suspect are key to the solution. The same basic rule should apply elsewhere, I imagine.
Perhaps the above is all absolute nonsense and you yourself have solved it in an utterly different - and correct - way. If so, do tell! Cheers