Oh believe me, I'd love nothing more than to reveal the full game code, I'm quite the show-off and terrible at keeping my own secrets, haha. But I've got some convincing reasons for keeping things close to the chest, and have thus far been able to resist giving everything away. The game is story heavy and very spoiler sensitive, and I'm planning to go full commercial release with this eventually. Also, the full code is nearing 10k lines, I think... I have released certain key pieces of the code in the past that I thought would be useful in others' projects, like the keybinding / input handling system, or the sprite sheet processor.
In the end, what I'm learning here is that the workarounds involved in getting rid of this slowness are either prohibitively laborious, or involve learning yet another new discipline. Which, I'm not against learning new disciplines, it's kinda what I've been doing the past two years in developing this game, after all! But a whole discipline for a one-off visual effect is overkill, so I think I will just have to come up with another effect.
The purpose of this thread is served, I got a convincing answer in the negative, and that lets me move ahead. I can still use the overlay for things that only happen once per frame, like the engine burnout and low-health alert. The slowdown was showing up when I fired a laser through 4+ enemies and they all had the effect going off at once.
Definitely was the clearcolor, though. I commented that one line out, and nothing else, and the slowdown vanished completely.