With Jin'rokh normal, your co-healers and you should be coordinating your CDs, so that you have a better feel for when to bloom them. Typically, we use the big raid CDs (Devo Aura, Healing Tide, Tranq, etc.) about 4 seconds into the Lightning Storm, to make sure people are topped off before/during the move to spread back out. As such, I boomshroom at about 2 or 3 seconds, depending on how well people are stacked, and how much health they have lost at that point. For Jin'rokh LFR, there is no coordination at all, so I typically ignore 'shrooms for the first Lightning Storm, since everyone and their cousin seems to want to blow their CDs on that one, and use them on the second one when people are at about 40-60% health. Another trick for Shrooms in LFR is to ignore them for Lightning Storms, and plant them immediately after a tank is thrown in the gray pool. Inevitably, a tank will take an extra Static Wounds stack, people will drop to below half health, and I will boomshroom on the stack of people in the pool. With the healing boost from the pool, and the amount of damage to heal, you get REALLY REALLY BIG NUMBERS! And lots of them.
For Ji-Kun normal, I use Shrooms as a big tank emergency heal, not for Quills, as people tend to be all over the place for that one. Stacking on Ji-Kun is generally a bad idea, what with Caw and Feed Young. When a tank is getting wrecked by stacks, I yell at them to stand on Shrooms and basically use them as a Lay On Hands on a 10 sec CD. They do not have to be fully charged to bring a tank from low to full in one boom. I do the same on Durumu to clear Arterial Cut. For Quills, I prefer to alternate between Tranq and Tree, and whatever my co-healer(s)'s CDs may be. Ji-Kun LFR, I am generally on the nest team, because I like flying!
Megaera, just use them on every Rampage when the raid as a whole gets below 60%. If they never drop, Boomshroom early so you have extra time to restack and charge them for the next one. By the last few heads, there will be plenty of damage for them to heal.