Dodgy knee, possibly a shoe problem, need advice please!

I searched before posting this, but nothing quite covers what I'm after. Any help would be massively appreciated!

Basically, I've been an on-and-off runner for 6 years now (18-24 years old). For most of these 6 years, I've gone through a pattern where I'd go away to uni, get lazy, put on weight, come home and then run it all off over the summer. For pretty much this entire time, I used one pair of shoes, which I've only just learnt is a bad thing. Needless to say, they were pretty shot towards the end and eventually got thrown out.

I graduated this December, bought myself a new pair of shoes and threw myself into running 15-20 miles per week. I started at 14 stone 10 lbs (93 kg) and got down to 12 stone (76 kg) within a few months, which I was really happy with, but started to get pains in my right knee for a few days after each run.

Being cautious, I rested up, assuming that it was just "wear-and-tear" from running whilst being too heavy. However, after rests of 1 week, 2 weeks, 3 weeks....it comes back immediately after the first run.

I'm starting to think that my new(ish) shoes are to blame. They've always felt a little unbalanced, like they are missing a bit of thickness under the ball of the foot. I obviously can't go back to my old ones, so I'm sort of stuck wondering what the problem would be. I'd only go and get my gait assessed as a last resort, because I genuinely don't think I have pronation issues and don't want to pay someone to tell me that.

If it helps, my old shoe was a cheapo Asics. Probably equivalent to a Patriot 4/5 now.

My new shoe is a NewBalance 690. Also cheap!

I don't know whether there are known issues with my new shoe, or if this is a common problem when switching shoes. Maybe my knees have gotten too used to the old shoe and I should get a carbon copy of the old Asics trainer? Or maybe I just should have taken it easier when I was at my heaviest and now have to rest for a few months before I'm back to normal?

It'd be such a relief to just buy a new pair of shoes and be running comfortably again.