Sorry I never replied. I sure had that same symptom... used the coolant funnel and when burping just random slow bubbles and they never stop.
Today I got a CEL when starting. It was cool, high 50s F. Stumbled a bit then CEL with VSC/Traction off (not really sure why traction control is affected?)
Anyways, hit up O Reily's on my way home to use the code reader, and sure as shit just as I suspected P0306 (Cylinder 6 Misfire), and P0456 (Evaporative Emission Control System Very Small Leak).
Came home and searched YouTube one more time because once again, my block test came back negative. And the very helpful Schrodinger's Box channel came in clutch... took 3 30 minute videos but are all very educational for anyone with a 4th Gen V6, especially 2003-2006.
2004 Toyota 4Runner P0306 Misfire Diagnosis - YouTube
04 Toyota P0306 Pt2-Can Compression Test Lie? - YouTube
04 Toyota P0306 Pt3 -Art of Puzzle Solving - YouTube
Now I am convinced I have a HG leak. I think the course of action I will take is to use BlueDevil radiator flush and leak fix fluid. A user here, can't remember his handle here, but Dylan from the YouTube channel Trail Benders Overland used it and posted a very good video of it
How to fix your Head Gasket for $100 with Blue Devil Head Gasket Sealer! - YouTube
Anyways, that video is far from the only Blue Devil success story, just the only 4th gen T4R that I could find.