The lesson is always the same: leave micro optimisations for later and spend more time learning about data structures that can improve your code locality.
For the super tight loops scc uses the micro optimisations still add up though so it wasn’t wasted effort and in the end it all came together nicely.
Before you have the features, you mostly want to find the boundaries on the problem so that you can slice it up into modules and optimize those independently. It's unusual in contemporary programming to have to do a whole-program micro-optimization pass, but that's the only kind you can do within a small program, so it's common to get the wrong idea and start shaving off bytes and cycles before the architecture is ready for it. In a large program, it's specific combinations of features that create performance spikes, and those tend to be addressed by building a new custom code path. When you scale up the data changes, so your view of the problem changes too, and you start being able to optimize by creating a codepath that combines a whole bunch of specific processing steps.