Sorry for your hard ship.2006 with 90k miles bummer. You can get a used engine from one of the salvage yards. Toyota pros in commerce city, Jims Yoda yard, yota yard in denver is great also. Have your mechanic go over it and you'll be fine. You can also browse Craigslist for folks parting out 4th gens. There are a few salvage yards around Denver so make some calls. you can also sell it to some one who may want to fix it up and buy a 3rd Gen 4runner instead with a bullet proof 3.4l motor.
There are quiet few Toyota independent shops get a second opinion like toy doctor in denver, toyexus auto repair denver, toy auto masters in englewood.etc look at their reviews call them get a price better then the dealer. The vsv valve is pretty loud on these trucks and that's what I heard on the video. I cant tell if it's what they say it is.