Everyone may need a different set of recommendations, but these few are a great place to start.
Avoid shoes that are too flexible in the middle. Wear shoes that have a stable midsole.
Replace old running shoes.
Consider trying more stable shoes than you've used recently.
Temporary decrease training. Stop if necessary.
Carefully examine your training regimen. If you've been keeping a running diary - check it for possible training errors.
In the future avoid the "terrible too's: too much too, too soon, too fast, too often, with too little rest.
These exercises are neurofacilitative. They improve the overall functioning of the quadriceps and the ability to work together.
The straight leg lifts may improve patellar tracking.
Start with 3 sets of 10 and work your way up to 10 sets of 10 at a moderately rapid repetition rate.
Perform 10 - 15 bridges.
After the bridges become easier, and only after your knee improves add in 8-12 single leg bridges.
Add in a few more core exercises, all of which can be performed in just a few minutes:
Hold your planks from 15 to 45 seconds.
Do some side planks. Add in v-ups. And you'll soon be feeling better, and may even have the beginnings of some firmer abs.
Posterior muscle stretches help the most.
Calf muscle stretches.