I've got a 99' V6 4WD 5spd 4Runner and it has an intermittent misfire in cylinder 4.

I replaced all the spark plugs and that didn't fix it
I swapped the plug wires where they plug into the coil packs and the misfire followed the swap (the code read for a cylinder 6 misfire)
So then I replaced all the plug wires and that didn't fix it
Then I replaced the coil pack and that hasn't fixed it

Here's what I don't understand. If it is the fuel injector, why would the misfire have followed with the wire swap?

When the engine has been sitting for a few hours and I start it up there is usually no misfire or choppy idle. When I start it up again after its been running for a bit the misfire and rough idle come back. If it is the cylinder or the fuel injector I can't figure out why the misfire would come and go.

 

After the misfire followed the plug wire to cylinder 6, did you switch them back to original to eliminate the possibility of a coincidence?

Hang a timing light on the misfiring cylinder and see what the strobe does. Missing spark events will be pretty obvious. If there are no spark misfires, then the misfire is caused by a fuel or mechanical problem.

 

That will work ^^^