Might need to bump the menalties slightly. The flaws as i recall were suposed to outweigh a feat so people didnt mini max themselves into a bunch of free feats. And considering pathfinder feats are more powerful than its a good idea to to make the flaws have a bigger penalty to compensate.
I found that they work pretty well so long as you pay attention to converting the skills that no longer exist in PF and, as Cliff pointed out, adding 1 or 2 points to the penalties to make sure the flaws are slightly stronger than feats.