I routinely modify every pair of running shorts that I buy. You should think outside the box and do that. Find a pair of running shorts that you like but are too long. Take them to a seamstress and have them hemmed. It shouldn't cost more than $5-$10. If necessary, she can also shorten the inside of the pockets.
In my case, the first thing I do with a new pair of running shorts is cut out the existing and replace it with a pair of performance briefs. Finding inexpensive shorts without a liner is relatively easy.