Are your hamstrings tight at the same time? I had a similar ache in the upper calf and it was the result of very tight hamstrings at the lower end, so where they are above the knee. The best stretch I found was to have my legs together, then bend from the waist so hands reach the floor, but not directly in front of your toes so you're making a sort of A-shape. Keep both feet firmly on the floor and hands on the floor with legs straight and hold for 20-30 seconds. Repeat 3 times a day.
Try lying on your back, looking upwards, arms out. Draw the knees into the chest together and roll to one side- hold there for about 10secs- but keep everything else in place. Roll knees to the other side and hold there as before. Repeat 5-10 times.
Tight glutes may be related to core issues- are you doing any core exercises such as planks? Check for suitable core exercises online.
The first has lots of useful info and advice as well as recipes. The second has many recipes if you get past the stuff about their 2-year-old. Look in the Running section as well as the Recipes section.
I have started having a similar niggle to the one you describe Khanivore. Have been to the physio for a tight calf that then developed (now much better), but the niggle is still there. Going to the podiatrist on Saturday and will report back. (I also have a leg-length discrepancy and wear orthotics)