Hi Holly,
If the pain is centrally under your knee cap it tends to suggest that there's probably no involvement of the ITB or the collateral ligaments, which generally cause discomfort at the side of the knee. I suspect it's unlikely to be the anterior or posterior ligaments either, even though they criss-cross centrally in your knee, as these are less likely to be aggravated by running alone. The fact that it came and went just as quickly (though is getting more intrusive) also suggests that it may be more to do with the way your kneecap is tracking over the groove formed by your femur-tibia joint.
While there may be some involvement of your knee cartilage (menisci) It sounds more likely to be the early signs of patellofemoral syndrome. This is not untypical in runners who do high mileages and have a tendency to pronate. It's also interesting that when you ran more on the outside of your foot (you were effectively decreasing your foot pronation) the pain subsided.
The fact that you have changed your shoes recently may also be significant for two reasons.
First, it implies your current shoes (which presumably are due for retirement) may not be having the same anti-pronating effect that they originally gave you as the midsoles may have deteriorated significantly - this would have a cumulative effect with mileage and may just have broken surface now.
Second, your new shoes, even though you are still breaking them in, may have antagonised your knee just enough to tip the balance.
Either way, if you can't see a professional then apply the usual RICE, use ibuprofen discriminately, try a patella stabilizing knee support - but make sure you get one from a specialist injury support retailer - not some cheapo off-the-shelf thing that may make things worse.
Regards, Groz