I recently jetted my 400ex to the right specifications on hmf. I have a hmf slip on and it starts fine and seems to run okay but after about 2 minutes of riding or just idleing for about 3 minutes the headers start getting very hot and glow red. I am not sure if it glew red before i dont think it did glow red before.

 

Try a 40 or 42 pilot jet.

 

You rejetted, did you change the needle setting?
The jetting suggestions from HMF are just that, suggestions. The techs at HMF don't know where you are riding, ie: elevation, area of the country, their suggestions are a starting point.
You are obviously runnuing lean and need to make some adjustments.