To follow your structure:
1) SLT doesn’t matter in the whole fight. It doesn’t make or break the encounter if the raid doesn’t make mistakes. You can (of course) correct errors, or soften certain hits. I put SLT there because its often used to catch people from the burst. The reason why I recommend Healing Tide, is because (as mentioned before) the fight with your group lasts 7,5 minutes. This means you can use healing tide 3 times in the fight, if you can find good moments for it. If you look at it like that, you have to find a moment latest .40 seconds into the fight to use it. Out of those 40 seconds, the first shadowfel burst is the best moment. This is also why I made the cooldown overviews. It is to maximize your cd’s given your current kill times at moments where the raid is actually benefiting from your healing. And yes, I often precast Healing Tide there, and that is a very good thing to do to optimize the ticks.
2) Pop SLT whenever it makes sense. Its not needed anywhere, so use it at your convenience. The reason why Ascendence is on first shackles is again cooldown management. You’ll need it up at the 5 minute mark, and for that to happen you need to pop it latest 2 minutes. Which is the moment the first shackles spawn (that is if your group pushes to phase 2 after 1 shadowfelburst – which should be expected at this point).
3) No, don’t use ascendance in the nether. Use it before. You should not pop cooldowns in there, and neither am I suggesting that. What I am saying is, convince your raid leader that you need to be outside for the first Rain of Chaos, so you can use Ascendence on the raid. Go in the nether if needed (which probably isn’t needed to begin with), and then pop your Healing Tide on the second Rain of Chaos. Given your logs this should provide the raid with the healing they require at the moments they need it. I don’t know how it exactly times out.. you’ll have to find out. I haven’t been in the nether in heroic/normal in ages. We always skip it. On Mythic, the whole raid spends have the fight in the nether so that’s different.
4) Dealing with healing cooldown orders – I recently responded to someone about this same thing. Check my response to this post for more info on this: https://chainheal.com/forums/topic/719-ilvl-looking-for-any-and-all-feedback-guild-starts-mythic-hfc-in-a-week/. I am working on something else in this regard, but it isn’t finished yet. Keep checking in on the site for this :).