You'll want to trench that hardware cloth in, about a foot deep (at least) to keep the critters from digging under it to raid the hen house.
We did the same thing on our garden. Used to get all kinds of critters in there. Here we just go out about a foot, and then use the abundant rocks to make a barrier on top of the hardware cloth. Seems to work pretty well.
The fencing is going to be kind of ridiculous. I'm using a 2x3 heavy gauge fence around the run and then putting the hardware cloth on. Mainly because the hardware cloth will keep the rodents and snakes out, but I think a coyote could pretty much rip right through the hardware cloth if they really tried.