I did mine with the truck running. A lot of guys take the manifold off and do it. My placement was on a flat spot on the top side of the manifold. First, I had someone cover about 95% of the tailpiple with a 2x6 to create some backpressure. Drilled a little ways, and kept dipping the drillbit in grease. I'd drill, clean bit, regrease, over and over until I broke through. Then with the engine stopped, I tapped it. Used a little grease on the tap, then used a small magnet to feel around inside the manifold for any shavings. Put the prob in, fired it up. No problems in the 15K miles since them. I routed my hoses and wires through a plastic plate that covers the hole where the clutch assembly would be if I had a 6spd.
I think I've got some pics in my readers rig gallery.
Hope that helps.
Andy