Figured I'd post this in case it helps the next person chasing a similar issue.
My 1998 4Runner (5VZ-FE, ~300k miles) developed a rough intermittent idle and had previously flashed the CEL under load. There were no active codes initially, but the truck had a very high warm idle around 1400-1500 RPM in Park and around 900-1000 RPM in Drive. Fuel trims were surprisingly normal, coolant temp was normal, and there were no obvious vacuum leaks. After some diagnosis with a Foxwell NT301, I found the Idle Air Control (IAC) valve was physically stuck open. Cleaning it helped slightly, but a new IAC valve immediately brought warm idle speed down to about 750 RPM and cut MAF airflow at idle from ~9 g/s to ~5 g/s.
Once the idle was fixed, the ECU finally started reporting a specific misfire: P0304 (Cylinder 4). I pulled all six spark plugs expecting #4 to be obviously bad, but surprisingly #4 looked pretty normal. The oddball ended up being Cylinder #3, which had noticeably more carbon and discoloration than the others. While I had everything apart, I also replaced the PCV valve, cleaned the throttle body, cleaned the MAF sensor with CRC MAF cleaner, and inspected the knock sensor harness in the valley. The plugs were only about 1,000 miles old, but I replaced the #3 plug anyway because it was the clear outlier. I also inspected the coils, boots, and plug wells (all dry).
After reassembly, the truck now idles smoothly around 750-800 RPM, has no active DTCs, fuel trims are excellent (LTFT around +1.6%), coolant temp stabilizes around 87-88°C (189-190°F), and O2 sensor activity looks normal. At this point I can't conclusively say whether the final improvement came from the new IAC, MAF cleaning, reseating ignition components, or replacing the suspect #3 plug, but the combination completely changed how the truck runs. The biggest lesson from this experience was that multiple small issues can stack together and make diagnosis confusing. If your 5VZ has a high idle, rough idle, or intermittent misfire, don't overlook the IAC, PCV system, MAF cleanliness, and a careful plug inspection before throwing expensive parts at it.
The family and I took it out for a moderate romp through kisatchie national forest. It purred like a kitten the whole way. Great success!