It seems odd to leave out just two of the group, and I'm not convinced about the "two others" yet. I felt that elaborating further risks theme spoilers, but now that the prize date has passed perhaps I can risk a little in order to discuss this further. I'll still try to be oblique, but anyone still wanting to work out the theme for themselves please don't read on!
Thanks dsc for pointing out clue 7 -- I think that might actually be row 7 rather than one of the "two others"! But I still can't see what might be a reference to row 10...
So I can just about persuade myself that:
* 25 "jovial" may refer to row 1;
* 21 "queen" may refer to row 2;
* 31d "fighter" may refer to row 3;
* 16 "spear-thrower" may refer to row 4;
* 17 "musical" may refer to row 5;
* 23 "messenger" may refer to row 6;
* 7 "animal goddess" may refer to row 7;
* 5 "of crops" may refer to row 8;
* 38 "of wine" may refer to row 9;
* 8 "lover" may refer to row 11;
* 9 "metalworker" may refer to row 12;
Being a little nitpicky, the subject of 39 is not of the same type as the group, so I don't think they can be one of the "two others".
I wondered if the first four words of the clue for 11 might refer to "two others" namely H-- and P--, but H-- has already been used by that clue as a place so that seems a bit weak.
Can anyone fill in any gaps and/or correct any misprisions above??