Whenever replacing the engine mounts on front wheel drive vehicles, you should always replace them all at the same time. This is for several reasons. Two of the mounts on that car, hold the weight of the engine (support the engine from the car body). As the vehicle ages, those mounts slowly collaspe down. This causes the two mounts that control the engine movement to streach and allow more engine movement then should be allowed. This allows parts of the engine (mainly the Exhaust system) to come into contract with the body of the vehicle and create a lot of noise.
Also as the supporting mounts collaspe, they no longer are isolating the engine from the body and allowing a considerable amount of engine vibration into the body, again causing a considerable amount of noise.
The reason that this is key on a front wheel drive vehicle (and less so on a rear wheel drive vehicle) is because the entire drive package is supported from those points. They not only have to support the engine and transmission, but are also used to control movement from the power package transmitting power to the ground.
On a rear wheel drive vehicle, you will have (at least) three mounts holding the power package to the body, but none of them have to control as much engine movement, as the power is applied throught the rear differential.
Also make sure that the lower rear mount is clean and free of rocks and dirt. This is one point that tends to get contaminated due to its location.
Actually, he has since replaced them all but the noise is still there. We KNOW that it has to have something to do with the engine mounts and he has heard of another person with a Ford Focus that is having the same problem but since his car is a "work car" he is willing to deal with it. My car is the only car I have. (I am FAR from rich.) I am concerned that this is a problem for all Focus' and that we should be doing something else to rectify the problem.
If all the mounts were replaced recently, I would be looking at the alignment of the mounts. If they are not aligned correctly, then a considerable amount of noise will get transmitted into the body.
Also like I wrote above, check that lower mount mounting location. If a stone or dirt has gotten in there, or the frame in that area is damaged, then that can also cause a problem.
I am hoping that you used Ford mounts.