Fairness of Cowry Shells as Dice
This has been a problem since the days when dice, hand-carved out of sheep's knucklebones, could never be considered mathematically fair. Historically, there have been two principal ways of improving a game:


Make sure that a particular number is not always good or always bad. In Craps, rolling a 7 is good for the shooter on the first roll, but bad thereafter; a slight unevenness making 7 more probable is not likely to materially affect the chances of winning, which it might with a simpler rule. 
Where possible, make results comparative not absolute. To decide randomly who starts in a two-player game, it would be possible to roll two dice and choose based on even or odd; this is 50/50 if the dice are fair, but not otherwise, so it is rare. Each player rolling the dice and the higher result starting is common, giving even chances no matter what unevenness there may be.


I would also suggest using all the shells every roll if possible; it is annoying enough waiting for those players who carefully select the "high-rolling" or "low-rolling" dice each time, without the possibility that they might actually have a point.