But as someone who has been modding games since the early 2000s, whenever performance issues come up, disabling the mods is usually my first step when diagnosing issues. The author explains why this wasn't his first instinct (given the warning signals), but testing from a vanilla state is always a good methodology IMO.
“My installation is non standard” should probably be disclosed early.
It's like if someone wrote up a post detailing a step-by-step teardown of their vehicle's engine to determine why they were suddenly getting worse gas mileage, only to end with "oh, you know what, it's probably the giant always-open drag parachute I installed right before I started getting bad gas mileage. Let me try removing that now that I've ruled out every accessible part of the engine."