OK, I forgot to put the link to my pictures.
http://rides.webshots.com/album/5765...navtype=search
I passed over this thought because you mention 3500 mile oil changes.
The 98-2002 Sienna is in the "gell" issue years.
A oil change interval that you mention "should not" have an issue, but it is possible.
Causes of oil sludge are long oil change interval, mileage or time, and another thing that really should be checked is the PCV valve.
A clogged PCV valve will cause problems in short order.
The PCV valve is in the rear valve cover, toward the passenger side end.
When you remove the oil fill cap, you will see a baffel, so you cannot see the valvetrain.
The baffel is coated with a rough black substance that looks like baked on sludge, but it was there from the factory as some sort of sound deadener.
To determine if you have sludge, you would need to remove a valve cover.
A synthetic oil is also benneficial in this motor.
A lubrication issue is a possiblility for the sound.....It was not my first thought because of the frequent oil change interval you mention, however folks have claimed to change their oil that frequently and still have the issue.
It is estimated that only a small percentage of all these motors (and there are a LOT of these motors out there in many different TOYOTA and LEXUS vehicles).