Try this:
1) Remove the K&N and reinstall your factory air box and filter.
2) Clean the MAF sensor
3) clean the idle control valve.
If it runs fine, throw away the K&N. I had nothing but problems with my truck and the TRD Oiled air filter (same thing as the K&N). The oil from the filter coats the MAF sensor and causes the ECU to incorrectly read the incoming air. This will cause the ECU to inject the incorrect amount of fuel. I had to clean up the MAF and ICV about 3 times, then went back to a stock filter. Never had the problem again on my '01.
check this link for a how-to
Toyota Maintenance: Tacoma & 4Runner 30K Mile Service