Anyone who has farmed instances for their Item Set Skills knows the feeling of how loot tables seems to get stuck on giving out the same item from the boss every run. So, in the interest of making it easier to farm ISS and to make use of every run to feel like you are progressing even when you don't get the items you want, I propose the following few suggestions. Any one of them is a viable solution this (depending on how easy do you want this to become):
1) A contraption at the beginning of the instance which accepts 3-5 ISS equipment dropped from the last boss only and you can select one piece of ISS equipment that will be the reward given from another contraption at the end of the instance, after the last boss has been slain. This makes sure that people are able to run the full instance and therefore will be able to get the equipment needed, it will just take a long time, so might as well make it easier. You can make it easier/harder by changing what is accepted by the contraption: the number of ISS equipment, whether the equipment has ISS intact or not and whether the equipment has the stats on it or not.
2) A contraption at the entrance of each boss run which accepts 3-5 ISS equipment dropped from that boss only and you can select one piece of ISS equipment that will be the reward given from this contraption after the boss is slain. This makes the farming faster as you only need to run +1 more times than however many items are needed by the contraption to have the full set you need.
You can make it easier/harder by changing what is accepted by the contraption: the number of ISS equipment, whether the equipment has ISS intact or not and whether the equipment has the stats on it or not. You can also make all the rewards drop from the last boss's contraption instead if you think people can exploit it for any reason.