i had the same problem with my 98 es300. using an existing air intake tubing i just extended it into the fender with flex tubing and hooked up a k&n oval round filter at the end (to make it a CAI).
at first i didnt get the check engine light, even after driving it for ~300mi at 60-75mph. it wasnt a week later til i got the check engine light. i then reset the ecu and efi by pulling the fuse and disconnecting the battery. when i hooked everything back up and started the car, the car seemed to hesitate (like it was struggling to suck in air...and almost surging). so as a temporary fix i disconnected the flex tubing and just connected the filter to the intake tubing (regular intake) and after a day the check engine light disappeared. i know should have taken it to autozone and got the codes pulled, but i didnt have time.
after reading your post, just thinking maybe we had the same problem