it should not hurt to nurse, no matter how long baby hangs out at the breast. Some mild soreness after marthathons, OK, but not so bad as you are indicating. Pain indicates a poor latch, which could also explain poor milk transfer and consequetnly the long feedings and not great weight gain. Also giving bottles unfortunately can contribute to a poor latch.
This is why Dr. Jack Newman always insists that, when there are weight gain issues, the first thing to do is assess breastfeeding via observation and hands on assistance, preferably by a breastfeeding professional (such as an IBCLC) and not supplement as a first step (unless of course weight is seriously off and baby requires supplements immediately due to health issues.) Many moms (probably the vast majority) whose babies are gaining amore slowly are told to supplement as the first course of action and never assisted in any other way. It's very frustrating as this often leads to a premature ending of breastfeeding, a serious health issue.
As far as it affecting milk supply to change nursing habit-I am still not convinced the issue is milk supply but whatever-on the one hand, when a mom needs to INCREASE milk supply, switch nursing (nursing both sides per feeding) is recommended. But otherwise, feeding on one side per feeding is fine as long as baby is satisfied. If you are nursing more frequently overall, it becomes less important supply wise to feed at both sides per feeding. Whatever you do, start nursing on the least sore side first and try different techniques for fixing the latch. Also make sure you are gently applying purified lanolin or another good nipple cream after every nursing session, shower, etc. For latch and positioniong ideas, Look up laid back positioning aka biological nurturing, breast sandwich technique, ameda latch video. If you want, post here a description of what exactly is happening pain wise (describe the pain, when it starts, does it lessen or intensify during the feeding, how long it lasts, is your nipple misshapen after nursing etc. and I am sure some moms will have suggestions. Or even start a new thread just to tackle the latch issue.
As far as weight goes-sorry nothing makes sense to me except pounds and ounces. Can you tell me how many ounces did baby gain in the days just prior to supplementing and then what baby gained since supplementing in how many days? Babies this age average about an ounce of gain a day. Going up in percentiles is fine, but there is a misunderstanding out there that going up in percentiles is necessary to indicate adequate weight gain. But that is not how growth charts work. Unless the baby starts out seriously underweight, as long as baby stays on his own general percentile (curve) or goes up, he is probably growing fine.