There is literally a "heat shield" under the shift boot, which is about 4 inches from where you describe, is the shield missing? I removed mine on my 97 civic because it was rattling at idle but I never noticed heat, but then again being 6ft I don't rest my leg there while driving.
I doubt its the cat, at least in the USA the d16 catalytic converter is on the exhaust manifold itself, never heard of a D series civic world wide having a "under car" catalytic converter, but it could be because different emission laws....