How to tell when it's too rough

I have two dogs and one cat and one of the dogs, Tojo, really likes to play with the cat, Hester. Tojo is a shiba inu who weighs about 20 pounds. He's very prey-driven and likes to chase Hester when she runs, and at first I was discouraging this and teaching him not to bother her, but she started to chase him, too, or run past him several times until he chased her. They sometimes take turns pinning the other one down and I have often seen Hester biting Tojo's neck or swatting at him from a high perch (he doesn't mind). They mouth each other and wrestle a lot.

Sometimes, however, I can tell the play is not well received. Sometimes, Hester runs away not to play, but to get away from him. Luckily, there are several places where he can't reach her, including a shelf in my linen closet which has her crate with a blanket and her food dish, so she hangs out there a lot. He's never given her any wounds, but sometimes I hear her squeak, then she usually swats him and he backs off enough for her to run away to somewhere safe. A few times, he has picked her up by the scruff of the neck and carried her, which doesn't seem to hurt her, but it's so scary to watch! I don't think she likes it, but she doesn't make any sounds like she's in pain and she's never gotten any cuts or sores from it. Once, he had her by the scruff of the neck and was shaking her. I didn't actually see this, my husband saw it, but I was there and didn't here her screeching or find any marks on her when I examined her...

Now I'm wondering if I should ban all chasing and playing just so it doesn't escalate into something worse. Both animals are about two years old and have acted this way most of their lives with few incidents, and no injuries (I got them around the same time as a puppy and kitten). Also, they sometimes just snuggle on the couch or just lay quietly next to each other, and Tojo will even let Hester eat out of his dish with him (but not the other way around). I'm not sure I want to interfere with their relationship, but it seems like Tojo is a little too playful for Hester sometimes.

We have this trouble with the other dog, too. Tojo pesters him and tries to get him to play, but he's simply not interested. I don't worry about those two, though, because the other dog is 65 pounds. Tojo also acts this way with most cats he meets. He tries to play with them, but they usually swat him and hiss and then he gets frustrated that they don't want to play and starts chasing his tail or whining at them and wagging his tail. I guess my point is, he's not trying to hurt her, he's just very playful and Hester puts up with him, so he doesn't leave her alone. Tojo will leave a dog or cat alone if they demonstrate that they truly do not want to play, but Hester does want to play a lot of the time and even when she clearly doesn't, she usually but sits there and lets Tojo mouth her and sometimes runs away.

Although, he does know the "leave it" command and if I tell him to stop chasing her, he will, but that's not to say he won't chase her again ten minutes later. Also, I'm home all day and he's crated if no one's home.

So... what do you think?

There is nothing that you've described that I haven't seen within my household at one time or another. The one behavior that would have me concerned is the picking up and shaking, although if Tojo is 20 pounds, it is very doubtful that he could hurt Hester, as she is full grown.

Dogs can be trained to understand when they've gone too far, but it can take a long time, a lot of dilligence and total consistency to get them to that point. First you need to find a phrase that they understand that can apply to any situation. If mine step out of bonds, I use the phrase "that's enough" and use it whenever I want them to stop what they are doing, whether its playing too hard (my 2 dogs weigh 170 pounds collectively and can knock things over with their shear momentum), barking at someone walking by (thanks for the warning guys but stop the noise), etc. I've actually developed a set of phrases using the word "kitty": that's a kitty toy, not a doggie toy, kitty is sleeping you can't come up (to the sofa) now, leave the kitty alone, etc.

Use the chosen phrase consistently when you see the behavior that you want to stop and then watch them closely and teach Tojo her boundary. After a while, they get it.

It is outstanding that you got Tojo and Hester together as infants and it seems obvious that they have bonded well. But you probably want to draw the line around Tojo picking up Hester in her mouth. It's not that Tojo would want to hurt her, its just that she can do it by accident. Stopping the play altogether might break the bond they have and I personally wouldn't want to do that. Tojo will always be Hester's protector and that's a good thing IMHO.