I have a Gregory rucksack which seems to do the trick fairly well, but the best rucksack will depend on your body shape so it's worth trying on a few at a running shop and jumping up and down a bit. It was fairly expensive, about £80 from memory. A couple things to bear in mind are that running rucksacks aren't terribly breathable so they will make you quite hot so I'd tend to wear a layer less than I would otherwise, and secondly even a few lbs extra weight seems to make a big difference to how easy my run feels. If you're planning on changing at the gym, it might be worth investigating how much it is to hire a locker there as my current commuting strategy is to leave clothes, shampoo, shoes etc at my locker at the gym the day before, then run in with a belt thing which carries keys, phone and oyster card. Alternatively, running home and leaving stuff in work tends to avoid the logistical issues of getting work clothes to the right place, but running into work is a great way to start the day and is actually quicker then getting the tube.
I get migraines generally starting with flashing lights, progressing to feeling sick then an intense feeling of pressure which lasts a day or two. I also tend to get problems 'finding' words and with spelling if I try to work through it. There doesn't seem to be any one trigger, but a combination of too much caffeine, missing meals and stress seem to bring on an attack.
When my migraines started getting particularly bad I was referred to a neurologist via NHS who went through some tests with me to make sure it wasn't anything worse (ie like a stroke, I'm not implying that migraines aren't bad enough) and I ended up with a prescription to take when I feel one coming on which seems to help. Maybe you could try and get a similar referral?
One other thought is that I recently started grinding my teeth which gives me headaches. It might be worth a visit to the dentist to see if it's anything like that, particularly if your teeth or jaw feels sore in the morning.
This happened to my kayano 17s too, with holes appearing within a few weeks of me buying them. That said it doesn't seem to affect the fit and I haven't been getting blisters so I haven't given it too much considereation - I'd just assumed that it was something to do with the shape of my foot (I have very long narrow feet).