Ironicly, letting the Clan War Matching function run more than 10 minutes seems to cause it to pick worse and worse matchups the longer it takes to finish. So far the clan matchups I've had were less than 10 minutes (even if I had to stop and restart) and all have resulted in less screwed up matches.
Also, never had to reset the search ever since I had clan war times to start at Noon G.M.T. (or 8am E.S.T. in the US) I guess more people in the world are up during that time, which gives more choices.
Anyway, this thread (
War As Scheduled, Automatically) was to answer schedule drift on constantly warring clans, but it can help with the issue of bad matchups.