Here's the solution. I've done this for a decade and it works better than any of the above fixes.
Find a brand and size of athletic performance underwear that fits just the way you want it and is made of a fabric that wicks moisture away from the body. These come in all sizes... bikini briefs, regular briefs, 2" legs, and compression short length. Asics makes a great running brief for $20, but I found the Champion Performance line to be just as comfortable and comes in short (2" legs) and long (8" legs). When I saw these on sale at the outlet mall, I bought 12 pair.
Once you find a comfortable brief, cut out the liner of the running shorts carefully to avoid cutting out any key pockets sewn to the liner. You don't need the original liner. I never run in the original liner anymore.
If the waist and length is right, I can ignore whether the liner fits right when I buy new running shorts. I routinely cut out the liner in all my brand new running shorts anyway.
Another advantage of this approach is that on a cold day, you can just switch to the 8" inseam briefs and have the perfect fit every time.