What model and brand scan tool are people using to clear things such as the egr code that is associated with the HO manifold swap on the 2.4?

Actron probably has the most complete line up of code readers.

The CP9125 Pocket Scan, just reads the active codes and will clear them. It's about the least expensive model, about $60 to $70 depending where you get it and if it's on sale. (I'm working on the cheap side with this one, it does what it's designed to)

The CP9135 is their mid level model. It does the same as the CP9125, plus it gives on screen code defenitions and displays emissions status. It costs about $150.

The CP9145 is their full function scanner. It does all that the CP9135 does, plus it will display live sensor data, displays freeze frame data, has help screens and will read stored codes(not active) of problems from the past. There are also upgade cables to read OBD I codes, if you purchase the cables. Costs about $270+, the OBD I cables are about $35.

The CP9150 is the same as the CP9145, except it comes with the OBD I & II cables and a case. This kit will cost about $380.

There are also a number of PC, Laptop & PDA compatable software & cable systems and vary in function. Most will display multiple sensor readings and give the DTCs. The prices will vary, some have the software for free, but you need their cables for it to work. Some have been discussed on this forum and in the Maintainance Forum.