After playing CoJ through Ascended AQ40 and high M+ keys, I personally don't find I have the issues that you have.
I think maintaining the 3 stacks is very forgiving. If your stacks drop before a boss, it takes 1 holy shock on a random person just a few seconds before the pull and then a judge + shock on the boss as you run in and you're back at 3 for the start of the fight. Maintaining the stacks in M+ is extremely easy as you're almost constantly in combat.
I've also never had a single problem with self healing ever. You can just toss yourself an instant flash of light and most of the time, Circle of Healing is all you need. You also can just Beacon yourself.
Speaking of Beacon, I don't even use the RE to extend the time as I feel like 1 global per minute during a fight is not a big deal at all... Sometimes I also just drop Beacon if I need other utility like Aspect of the Pack or something in a key as it's not that impactful.