If you're going to do a project anyway, this would be a good time to really do some thorough experimenting if your friend will let you.
Factoring out incubation and diet issues, what I would do is:
1. Single breed them, and mark all the eggs. Legband or otherwise mark the hens with numbers/colors, and mark the eggs from each hen. Set up a small pen for each hen and rotate the rooster amongst them every 2-3 days.
2. Track fertility - any hens have no eggs develop? Less than 25%? More than 75%?
3. Of the ones that develop, then track which ones die early, which ones die late, and which ones hatch successfully.
Armed with the above info, you could focus on only setting from fertile hens that produce viable offspring. Further along, you could branch out into putting the sire over his daughters and the cockerel of best type over his mother/aunts and then track it all again. Given enough time and diligence, this would at the very least tell you much more about what issues are happening, and at best could really increase fertility and hatchability over a few generations.