I just took mine off to reveal the "hood recall cuts" and I painted mine and stuck it back on. It looks GREAT now since I painted it. I just used black spray paint and did a few light coats.
I was wondering the same thing about the holes. I took the blanket off a bit to see if it was painted under the hood, (incase i did want to take blanket fully off) and saw the holes and was curious to what those were for. I'm just happy the underside of my hood is painted along with underside of doors I have read that the 2003 cobra's arn't and nor are the underside of the doors, don't know about the 1999 or 2001's
I'm not positive about this, but for certain classes of car the NHRA and IHRA requires the hood blanket as a safety feature. I'll be up at Epping in a couple weeks and I'll ask a tech guy, but if someone is going sooner, I'm kinda curious...
Mine has an ugly arse metalic looking thing for a liner. Looks like someone chopped it up to make it fit the 96 Cobra Hood. Problem is they covered the back vent holes. I originally took it off to cut holes in the liner for the vents at the back of the hood. But I personally like the looks of the hood a WHOLE lot better without the liner. Maybe a stock one is different??