Misfiring on start up and exhaust question

First of all, my truck is a 97 2.7 4x4. Questions: randomly about a month ago, the truck started to misfire upon start up but then evens out after about 10 seconds. The plugs are new, the wires are new, what else do i need to check? Second question, i have what i thought was an exhaust leak (i figured the manifold was cracked) so i bought a new LC header and cat, while it did have its benefit, that didnt solve the problem i was aiming for. The problem is under any kind of load i can hear the sound of the exhaust (not the exhaust note, but the sound the exhaust is making as its passing through the pipes, like a constant chh sound, but not a ticking. Hope that makes sense) through the firewall on the passenger side. Its more of a nuisance than anything else, but any ideas what that could be?