I think I've finally narrowed this problem down to something mechanical, but I'm not sure where to start now.

I have a slight hesitation around 3400-3700 at WOT. I confirmed this from scanning it and seeing the MAF sensor show a drop in airflow in this RPM window.

It is also the same range where I got knock on the nitrous.

Timing is the same through this range, as if commanded AFR, so it seems something internal is causing a change in airflow.

I actually also get a similar symptom around 4600-4800RPM.

Where should I look/what should I do next?

 

Have you looked at fuel pressure at the point the problem occurs?

 

Yep, a few times, and it looks normal, as do the O2 sensor values.