No...passing stones during a Liver Flush USUALLY does not cause pain... although there are exceptions to this. Following the Liver Flush recipe precisely generally eliminates most discomfort. You'll probably want to read through some post on the Liver Cleanse forum to get an idea of what to expect...and also ways of addressing things if you do experience some difficulty. Make sure that you stop the shakes the day before a flush and don't resume them for 1-2 days afterwards.
It can take several months to really cleanse the entire digestive tract...since you're already seeing some improvements I would stick with it for a while. Also, colonics...when done by a good therapist...are not painful...and are a great way to excelerate the cleansing process.
BTW...don't attempt a Liver Flush unless you've got a free day following taking the potions...you'll need to stay close to the bathroom and may not feel up to doing much of anything that day.