Interesting issue. Since you've already tried a different fuel tank and primer bulb and bypassed the fuel/water separator, it may be worth looking beyond the basic fuel supply setup.
Have you had the engine scanned for stored or pending fault codes? Even without a warning horn, checking the ECU fault history could provide some useful clues.
If possible, I'd also check fuel pressure under load and monitor live data, particularly throttle position and sensor readings, when the RPM starts fluctuating. That may help narrow down whether it's a fuel delivery issue, an electronic control issue or something else.
Does the RPM fluctuation happen at lower throttle settings too, or only after running at full throttle for a few minutes?