Did one of the follower missions to get a 630 item with 87% success, and it failed lol, and a failed a few others in the 80% range. So yeah do those epic ones with as close to 100% success as possible.
Now that tokens stack, keep them around. When you get one mission:
1) Wait until everyone is back from their missions.
2) Use the Mission Planner to build your best shot mission
3) Check who is orange to the mission, and figure if you have enough tokens to boost him/her (I don't think there's a difference between 616 and 618 for a 630 mission, for example, but there will definitively be one between 628 and 630, obviously)
4) If you have no orange follower, but lack a counter, it's usually because you have a follower with subsidiary boni that help and the followers with the counters don't have the level. Find out from the help list on the missing counter which followers has the highest ilvl to be raised, if you can.
5) If you haven't any mission whose reward is "mandatory", keep hoarding the improvements, and use the straight armor/weapon sets on followers who have the lowest (600, if possible) in that value
Side note: If you're using the Inn to pad your followers... recruit a couple followers with
High Stamina. It probably matters more in the end game than scavengers or anything else. One of my followers went rare today and got that one, which I hadn't paid attention to. She got assigned by Mission Planner to every 615+ mission that I didn't have all the required counters for.
Oh, and keep playing for the long term. I wouldn't be surprised if 6.1 let you raise your followers to ilvl 660 and raid Blackrock Foundry for you.