The issue with crate training is that they don't like being separated from us...it's not the actual crate, it's what they associate the crate with. So, the way to get them over that is to NOT use the crate only when you leave them, and to start when they are young. If you can have a routine that is predictable to them, that makes crate time more acceptable. So, the crate can be in the bedroom at night with you so they're still close, and in the kitchen when you eat, so they're close, etc. Eventually, they associate the crate with neutral feelings and you can leave them in it.
With regards to running..and I'm a runner...I never understood taking a dog on the run. I have never seen a dog in tow actually enjoying it, and I typically think the owner just brings them along to tire them out, as a substitute for doing something later on that the dog might actually like, perhaps a hike or some time in the park. That said, the issue with running with them isn't just the distance or their age, its the fact that they can't stop and over time, that can cause serious injuries..which they're most prone to when they're young. So, just from my perspective, I'd nix the run, you do that for yourself, and find time to do something they'd like that also doesn't pose any risk to them.