My son is currently in a state school achieving OK results and is now in year 5. End of year 4 results were Maths 5c; English 4B; reading age is apparently age 14.
Are the year 4 end of year grades good enough for applying to a GS? I have no idea what his predictions for the end of this school year are
Yes, they are, and he has done well to achieve those despite missing so much school. He would be expected to make a further two sub-levels of progress each year (on average), so his end of Y6 levels are likely to be 5a for maths (or 6 if the school does the Level 6 tests) and 5a for English. Both are the top of the range.
Do GS take into consideration mitigation for children who may not have performed as well at school due to serious illness?
No, they cannot. However if he doesn't qualify in the 11+, an appeal panel would certainly take that into account.
What age bond papers should he now be completing - up until now he has being doing 9-10 age papers and getting around 70-80%. Is this sufficient?
Those are pretty good scores, but see the next point ...
Is there anything specific I should be doing with him in order to prepare him for the exams?
You need to tell us which area/schools you are interested in because the entrance tests differ widely. We can then help with recommendations for appropriate materials.