There's quite a few people on here who run with dogs, and quite a lot of threads to give you some advice. I run with my dog, a collie/ setter cross and its his most favourite thing in the world. Ever. I've never ran him more than 10 miles or so, but he seems totally fresh at the end and doesn't even have the grace to pretend he's tired.
Be careful of the harness, I still need to get a proper one as the last time I used a regular harness and it bit into my dog's skin, which seemed to bother me much more than him. You can buy special padded harnesses that spreads the load more. I found that the dog is much better controlled in a harness compared to just a collar.
I always take enough water for both of us, but we generally don't get a drink until we're finished unless its very warm. I pack a bowl in the car, for him to drink from.
I clip his extended lead to my running belt as this keeps both hands free. I think the lead is about 6 feet long. Too long and you run the risk of tripping, too short and you can get in each others way. I actually made one up from some polyester rope, a dog clip and a couple of large key ring 'rings' so that I can change the length easily whilst we're running.
Personally I find it more tiring running with a dog as you're constantly correcting him.
Don't worry about all this though, just give it a go and see how you get on.
I've just remembered that Trail Running did a feature on this recently, they recommended the harness from canix.co.uk but the whole outfit was pretty dear.
If you already have a bike then you could buy a turbo which is a kind of resistance unit that the bike mounts to. They're a bit more realistic than exercise bikes and you can always take the bike off and go for a spin.
They don't work too well on mountain type bikes as you really need smooth tyres, but any old road (racing) bike will work.
Thanks SP. That all sounds logical. I'd thought that it may be due to the bouncing up and down, but hadn't thought of posture. I'll keep an eye on that. I've had a few ibruprofens over the past couple of weeks, which seem to help. I'll try taking them more regularly over the next couple of days and see if they clear it up.
I don't suppose that keeping running is helping at all. Maybe I'll try and give it a break for a few days.