Well then, I do have to alter my comments. You do need to level the foundation and pick high ground to avoid the entire run getting wet.
I built a similar all in one coop/ run on quite a slope - we had to dig down one end and fill in the other to get it level, and picked a spot that is higher...
I doubt they will notice 2-3 inches depending on how large the coop will be - but would be best to try to level the coop. People doors don't work well if they are not hung straight.
They don't have to have a level run.
And, Hello and , so glad you have joined us. You should consider...