The good news is that the achilles injury is on part of the achilles which has a good blood supply and that the injury itself probably isn't as bad as the pain occasionally suggests - around the insertion point although there is tendinopathy (and if any of this is wrong it's my fault for not remembering properly what Noel said!) but the "irritation" from the shoes is due to a small patch of hypersensitive tissue - basically that particularly bit shouldn't be lasting but just until it calms down. There's still a lot of work to get the achilles healthy but on the whole it's not as bad as might have been thought.
The bad news is that it and the strain on the outside of my foot are almost certainly caused by a complete lack of mobility and extreme tightness around the rest of my body. My glutes have apparently "gone to sleep" and are just totally non-functional almost when I run. My hip flexors are tight as anything so there's no way I'm driving my body forward properly. My hamstrings are... well... they're my hamstrings just as they've always been and roughly the same length as my patience in not running. I've got an asymetric pelvis which whilst not great isn't a huge worry apart from the fact that the tight glutes, ITBs, hamstrings etc. are exacerbating it.
So going forward - I have exercises and stretches to do. Basically along three main lines - 1) strengthen achilles (eccentric heel drops) 2) stretch out all my very tight muscles groups 3)reawaken my glutes and basically learn how to run properly.
On the plus side once this is all done then I'll be able to run possibly not looking like I'm on a long haul flight to the US and settled in for a long journey (I sit down - a lot) and hopefully a little bit faster/more efficiently as well.
My fastest ever 400m was oddly enough set the summer after I was badly enough injured I couldn't run more than a minute or so and ended up just doing a solid 20 minutes of drills each evening and sometimes 2-3 times a day. Almost immediately I came back and whilst I couldn't run aerobically for toffee I was much more fluid. Looks like I'll need to try and be more of a complete package now than the stereotypical marathon runner!
Whenever I think about it - it always shocks me how we're willing to throw ourselves into 10-12 hours of running a week and yet spend so little time learning "how" to run.
To the commenters (it's appreciated!):-
Aaron - Thanks for the support mate - miles will be down a bit temporarily but as long as I can tick over I won't be too frustrated. Seeing the progress you've made recently has been pretty inspiring stuff for the rest of us!
Anonymous - You're absolutely right. I'm working on it - probably having breakfast at least two out of five weekdays now but it's still not enough. Unfortunately I'm not a morning person. Once I'm running regularly in the mornings I think it no longer becomes even vaguely optional though.