I had the same problem on DC Sports stainless steel header on my Honda. It was cooking everything around it...I noticed decreased performance from my A/C and radiator. In hindsight, the gains from the header were being offset by the short style intake sucking in the hotter air.
I decided to wrap the header with the DEI product. I was absolutely meticulous so it came out very nice. The instructions specifically said not to wrap over any welds.
And was it worth all the hassle? Definitely. Solved all my issues.
That was back in '99. I sold it to a buddy when I changed engines in '01. I've seen it as recently as about three months ago and it still looks good.
So based on my limited experience, I say do it. However, you may want to talk with Wagner and make sure its not going to void your warranty.