Hi Grumpie, well done for getting started again. To improve its best to do different types of runs, e.g tempo runs, hill training, intervals, long slow runs, recovery runs etc. I'm not familiar with any 10k apps and don't know if there is science begin it. As you are looking to continue beyond 10k why not look at a beginners half marathon plan which will also teach you about the different runs? There are lots of them out there. Just have a look on google. I personally used http://www.bupa.co.uk/~/media/Images/HealthManagement/PDFs/Beginner%20half%20marathon_FINAL.ashx and also have a look here for the types http://www.bupa.co.uk/health-information/directory/r/running-programme-half-marathon
Regarding the pain, i know exactly what pain you mean as I also get it, but I have no idea what causes it and how to prevent it. I mostly get it on my faster runs, sometimes I can ignore it and continue, other times it makes me stop dead for a few minutes before I can continue with a slow jog.
Leave a pair of shoes at work ( if you can) which you can change into when you arrive, and take off before you leave. saves you from lugging a pair around. In terms of backpack, I would look for a comfortable running backpack, as comfort is important imo. If it's not waterproof you can always put your things in a plastic bag to keep dry before putting them in the backpack.
Mr Soft, just run straight towards them until you are almost running into them and then either, stop abruptly and shake your head or just at the last second go to one side but make sure you get to make contact with their shoulder/arm! I can't stand obnoxious people who think that they don't need to show some sort of consideration towards ppl around them.