I've had a JLT CAI kit for a while but what always bothered me was that the tube was touching the hot water pipe below it, therefore conducting heat from it - exactly what you don't want.

Do you have any advice how to minimize the head conduction. Perhaps some thermal foam or wrap around the water pipe??

 

I've had concerns about this too, my issues with the JLT after 40k miles are:

a) the cone filter has been rubbing on one of the brake lines coming out of the distribution box, enough to leave a wear mark. I'm concerned about long term abuse and possible failure of the brake line. Going to need to cushion this somehow
b) Where it touches the water hose, I lost the plastic cover they give you for it, so my water hose is showing a wear mark, just like the brake line
c) The metal ring has wiggled itself out of the plastic tube and bent down a little, seems to be from the weight of the cone bouncing around.
d) The plastic tube has developed 2 stress cracks from the metal ring falling out

still runs like a champ though

 

I had both these issues when I had my JLT.
Get some foam pipe insulation from Home Depot and 2 hose clamps on rad hose under the JLT. For the brake line issue I attached a metal L bracket to the top of the cone filter and bolted it to the existing Air box bolt to pull it away far enough.
This worked for me.
Or you could just upgrade to a Super Charger! Caution, this is much more expensive.