I can only speak from my own personal experience, although I think I was at a similar stage to yourself a few months back - and getting pretty frustrated by niggly injuries. I would say if you do have these sorts of injuries it is definitely worth getting some gait anlysis to check for any problems - for me heavy overpronation was part of the cause of these injuries when the distances I was running increased.
I would say it is you must listen to your body, and just take a couple of days off if something concerns you, and take it easier just in case the injury becomes more serious. I find it difficult sstill to distinguish between a potentially more serious injury and an expected niggle, but I gues sit's how you manage your niggles (?!) I must say also there were many occasions when I just wanted some sort of reassurance that these injuries/niggles were part and parcel of my body adjusting - in the end I just told myself they were and got on with it (carefully adjusting training volumes/intensity).
Also, it kinda doesn't matter how 'fit' you are, it takes frustratingly long for your musculo-skeletal system to catch up with your cardiovascular system - especially when you've been a couch potato for 10years like me and start some serious running. I've teetered on the edge of falling into this trap , and hence why it is very true that you can't train for a marathon from the couch in 16 weeks...! My first marathon that I never thought possible is next week10 months after being a 'I hate running' sort of guy. Couldn't have done it in a shorter time frame, and wouldn't have wanted to for the exact things you highlight - injuries that go a long with increasing running volumes.
Anyway, take it easy and keep listening to your body!
I was permanently injured for the first few months of running: nothing really major, but always some kind of leg pain or another. What solved it for me was concentrating on form and running several sessions very slowly. I also avoided running two days in a row for quite a while.
Although, of course, everybody's biomechanics will differ, and you need to run in shoes suitable for you, I personally believe that far too much emphasis is placed on using shoes to correct what is essentially bad technique. Attention to running slowly with good form can do wonders, with the agreeable side-effect of an improved aerobic base and strengthened muscles and tendons.
Also, I don't consider 7 miles @ 9 minute pace slow for somebody with your times. In your situation I'd try 10-11 minute mile pace for a while. Throwing in strides a couple of times a week to practise good form at speed and to ensure adaptation of fast-twitch muscles should also be beneficial (but keep the lengths of the repetitions short and ensure a good warm up and decent recoveries)
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