First of all, ahoy, and welcome aboard!

I believe Bobby (XVTer) has a manual tranny, so, he may be able to help out here.

You may also want to check out thenewx.org, if you haven't already.

Could be something as simple as a heat shield rusting off or as complex as an exhaust manifold. X's are notorious for cracked manifolds. I know they beefed them up recently but I don't remember what year it was they started. My first instinct is a heat shield though. I've had a couple rust apart and cling. They will do exactly what you're describing. Simple fix is to rip it off. Manifold will cost you between $700 & $900 to replace.