Thank you for all the replies
The gap between pad and disc is normally quite small anyway and may need to bed in a bit. (in other words wear down a bit) If when you changed the pad and disc the calipers were clean and their sliding pins were clean and free of corrosion they will probably settle down.
I cleaned the caliper, first with a wire brush, then with brake cleaner. I cleaned and re-greased the sliding pins with silicone grease.
You probably needed to push the brake piston/s back into their bores when fitting new pads which can raise the level of fluid in the brake reservoir, but done correctly there should be no need for bleeding the brakes.
Another possible pitfall when changing discs is not checking that the mating surface between the disc and where its bolted to the hub is clean and free of loose rust etc. Trapped crud may mean the disc does not run true.
I removed the brake reservoir cap and pushed the brake pistons back into the calliper. I also pumped the brakes afterwards. The fluid level did rise higher than it was when I started. I assumed this would go back down after using the brakes for a bit.
The hub was pretty clean to be fair, basically no rust. I did clean it with brake cleaner and then put some copper grease on the hub just to make the disc removal easier after the next 50k miles.
I'm not sure 'braking lightly' is the best approach after fitting new pads etc. The brakes will bed in quicker if you brake harder than normal for a while. ( allowing a bit more margin to allow for any temporary loss of efficiency) I wouldnt 'pussy foot' with them.. Give em some welly . Poorly bedded brakes may be sufficient for light braking but may not yet deliver 100% efficiency, should you need it in a hurry.
When I've had disc and pad changes before, the mechanic has always said take it easy on the brakes for a bit, so that's what I've been doing. But today I was a bit harder with them. Don't want to do an emergency stop just yet, but I'm sure some idiot will pull in front of me on my way to work tomorrow because I just jinxed it now.
No matter that I intend to drive minimising use of the brakes some twit BMW driver will pull across my path without signalling meaning I need to put the anchors on hard. 
Literally happened to me a few years back. Brand new brake pads/discs, and a new rear calliper on my old GD, and literally the roundabout after leaving the mechanics, someone braked hard in front of me all of a sudden, and I had to slam on the brakes. I watched the Dashcam footage back because you could hear me screaming "FOR GODS SAKE, THE BRAKES!!", haha.
Good work. That's exactly how I go about repairs. Having watched it done on YTube a few times and read forum posts etc gives me the confidence to have a bash. Think of all the money you've saved, Honda currently quote the repair at £700 !! https://www.honda.co.uk/cars/owners/repairs.html
Thanks, it took me about 6.5 hours to do, and I'm glad it's something I will only have to do every 50k miles, as it was a pain to do, but I was being overly careful, and cleaning everything and making sure I was doing everything right, so it was probably worth it just for that. Probably a more thorough job than I would get from taking it to a garage.
There is no mechanism to retract the brake pads; slight runout of the disk pushes the pads away from the surface but only the thickness of paper. At the moment your new pads will have a rough/hairy surface that is slightly rubbing the disk. When the brakes have been used for a while the surface of the pads will be much smoother and will not, (should not) rub.
Thank you, yes this makes a lot of sense. I'm just being paranoid because it's the first time I've done this myself, and it's something really important like the brakes!!
The brakes did feel a bit better today actually.
Fuel economy still poor, but I will keep an eye on that.