I'm replacing the engine so I will have access to the header and would like to check the exhaust system for leaks.  I was thinking that I would plug 5 of the 6 ports and blow a fog machine down the 6th port and watch to see if fog comes out anywhere from front to rear.  Is this a bad idea?  Would the fog from a fog machine damage the muffler?  Do you have a better way to test for leaks?

That sounds like it will work fine for big leaks as the exhaust system is cold, other leaks may show up as it heats up.

The only fog machine I'm familiar with uses glycerin. I have no idea if that's a problem or not with a catalytic converter but why not wait for the engine to be installed. Run it, then look for leaks by holding your hand near joints in the exhaust? If you can borrow a thermal IR gun, you'd "see" the heat escaping from a leak.

that sounds like a pretty good idea, i don't think the smoke machine can cause damage to the muffler... (but im not a mechanic :p).... be careful with the exhaust studs, some of them can be snap happy (especially that bastard cylinder 1 that snapped on me and i never fixed)