All vacuum leaks are gone, and the car's running like a top. The obnoxious whistle/whine came from the throttle body, not the intake manifold. Granted, I still found an improperly torqued bolt on the IM, but the TB...whew, that was something else. I had the pleasure of hearing it quiet down and disappear as I tightened down the four nuts/bolts, at least. My STFT/LTFT numbers are back within normal parameters, and several code scans before, during, and after normal and hard drives revealed no codes.
...Except one, actually. It's a mystery to me, but I threw P0660 (Intake Manifold Tuning Valve Open Circuit) after fixing the vacuum leak. No CEL ever came up; it appeared after conducting random CEL checks through Torque Pro. It never appeared during my vacuum leaks, which is a head-scratcher. To add to the mystery, I actually had my VTCS male adapter plugged into my only solenoid! I should've plugged in the white one, not the green one. That cleared up the code, and pepped the car right back up. And that was the end of my P0660 code!
Car's back to normal for now, so I just got to drop in those trailing arms, and I'll more-or-less be done with modding for some time.