2005 4Runner, 4.7L, 4WD. 90k miles. Same symptoms. Cold starts with a rough "whirring" sound then one day the CEL and traction lights light up and the vehicle will barely make it to 30mph.
Dealership runs codes and tells me the air pump is faulty and the valves (3 of them) will need replacing. Original estimate of ~$3,900.
Could not find after market pump or valves and my Haynes manual stated this is a complex procedure. So I went with dealership.
While at dealership I called Toyota and filed a complaint. Spent 45 minutes telling them it was the air pump and couldn't understand why some Sequoias and Tundras got extensions but 4Runners didn't. Was told they'd get back to me next day. Two days later I've not been contacted.
Final bill was $3,200. ($2,300 is for parts. $1,300 for pump, close to $1,000 for three (3) valve assemblies).
I obtained the faulty part and the blades on the impeller are constructed of a cheap plastic that over time became brittle, broke off and the pieces got stuck in the valves.
For such a crucial part that owners can do nothing to maintain, Toyota should admit to using a defective part and extend warranties to 4Runner owners too.
Edit to update: Three days past contact with Toyota and they have not responded directly to me yet.
Edit to update (2): Heard from Toyota and they are refusing to extend warranties on these parts for 4Runners thus far. However if other 4Runner owners encounter the same problem please report them and conditions may change.