I just want to preface this by saying that I am definitely still greatly enjoying this story, and none of this will cause me to change my Wednesday evening habit of checking SV every 15 minutes or so.
I think that one factor that has contributed to some of the difficulty in pacing is that the rate of power growth is possibly too high. Aperion goes through 2 or 3 complete game changer power boosts between each major plot point. That makes it harder to plan on the future, and the last minute shifts makes it so you are having to adapt on the run much more often. It probably doesn't help that sometimes, by the time Aperion has finished pondering his new power, he is already halfway to the next new one. I think that the rate worked well earlier on when he was starting from nothing, but with how the powers all have compounding effects, there are so many drastic shifts in his power level and capabilities that keeping up with it is hard (and of course it means that something that seems like it should be major can get overshadowed before it gets a chance to be shown off in practice). It might be worth considering reducing the frequency of power growth now that Aperion has reached a fairly high level. He can still improve over time, but I suspect there are also a lot of things from earlier powers that he just never explored that could still boost him without being a new power.
The other problem is that to compensate for his massive growth rate, you have had to pile more problems and adversaries on top of each other, rather than having him deal with them sequentially. While this is good for keeping him challenged (time being his biggest problem), it makes it harder to balance all of them. This story isn't really following the more traditional worm fanfic arc structure, because it is just more problems all getting piled on at once to give him a challenge before the earlier ones get solved.
I'm not sure if slowing down his power growth would hurt your ability to write (I know you have said it helps you maintain your rate), but it might worth thinking about trying reducing the growth rate for a bit. That would give you some time when things are less unstable to fix up any of the things you think might be causing some of the structural problems, which might help. Or you could just keep going as is, and I will still enjoy the ride. I don't really know how well qualified to give writing advice, but it is something to think about.
I think that one factor that has contributed to some of the difficulty in pacing is that the rate of power growth is possibly too high. Aperion goes through 2 or 3 complete game changer power boosts between each major plot point. That makes it harder to plan on the future, and the last minute shifts makes it so you are having to adapt on the run much more often. It probably doesn't help that sometimes, by the time Aperion has finished pondering his new power, he is already halfway to the next new one. I think that the rate worked well earlier on when he was starting from nothing, but with how the powers all have compounding effects, there are so many drastic shifts in his power level and capabilities that keeping up with it is hard (and of course it means that something that seems like it should be major can get overshadowed before it gets a chance to be shown off in practice). It might be worth considering reducing the frequency of power growth now that Aperion has reached a fairly high level. He can still improve over time, but I suspect there are also a lot of things from earlier powers that he just never explored that could still boost him without being a new power.
The other problem is that to compensate for his massive growth rate, you have had to pile more problems and adversaries on top of each other, rather than having him deal with them sequentially. While this is good for keeping him challenged (time being his biggest problem), it makes it harder to balance all of them. This story isn't really following the more traditional worm fanfic arc structure, because it is just more problems all getting piled on at once to give him a challenge before the earlier ones get solved.
I'm not sure if slowing down his power growth would hurt your ability to write (I know you have said it helps you maintain your rate), but it might worth thinking about trying reducing the growth rate for a bit. That would give you some time when things are less unstable to fix up any of the things you think might be causing some of the structural problems, which might help. Or you could just keep going as is, and I will still enjoy the ride. I don't really know how well qualified to give writing advice, but it is something to think about.