All the dots are on the water pump housing. Check the alternator also,
directly below the water pump. Try removing the drive belt & see if the
noise goes away.

 

It's been over a year since the last reply to this topic. I have the same rattling that started this tread. I am going to get an oil change tomorrow and I will ask them to check the heat shields. Hopefully its a minor fix.

 

Well I got my oil changed and had JM Lexus check out the rattling noise. They found the problem..right side exhaust manifold heat shield and the right side A/F sensor heat shield were touching. They repositioned the A/F sensor heat shield and exhaust manifold heat shield. Problem solved!! BTW they didn't charge me. SWEET! Thanks JM LEXUS.