Q: My car has several misfire codes and does not run properly.

Hi there. What prompted you to replace those particular parts? Did testing reveal a fault? This year model, along with its sister IS models, up to 2011 had a service campaign for cylinder misfires. The campaign did not cover the testing for the condition, but it did cover if the testing revealed results according to what was specified. Unfortunately, Lexus began phasing out this campaign several years ago and the 2006 model has been a casualty of this phase out. There are some things not related to the campaign that can cause your misfires and possibly lead to the "limp" mode you stated, how was the "limp" mode determined? Many times, the oil control valves for the VVT become worn or contaminated and begin to stick; I believe this is the case with yours as the misfires are all on Bank 1. Remove the oil control valve and see if it is pretty easy to move, if so then the filter may be clogged; this filter is located in the port where the metal oil line attaches to the valve cover. If it feels at any point that it may be sticking, then it needs to be replaced. You may need to clean the filter and reinstall; if there is no filter, it has to be replaced as this is what protects the oil control valve. I highly suggest a fresh oil change with the proper oil and filter and use only premium fuel; using regular fuel grade is what led up to the service campaign correcting carbon buildup on the valves and pistons. I suggest having a qualified technician perform an inspection to avoid replacing unnecessary parts. Your Mechanic has several available technicians that can assist you with a check engine light inspection.