WOW...I don't recall seeing those felt padding at NB copper base and screw inserts.
Asus much revised it already
What was the temps at stock (before) modding?
First, put the heatpipe on the table top, face down as like you install it on the mobo, check for the flatness, make sure the SB/NB & MOFFET copper bases touches the table surface. If it's not then just straighten the pipe, use your thumb to push it downward on the pipe.