The engine seemed to be running ok (ran smooth, plugs looked good, etc), but there was something else obviously wrong. Carlos did a compression test and discovered that cylinder 4 was low by about 20%. A little oil in the combustion chamber raised the test numbers; he theorized that the rings were bad in that cylinder. The engine was removed from the car to be torn down and rebuilt. After dis-assembly, the issue was confirmed: the compression ring on piston 4 was broken. Thankfully, the pistons were not damaged, and the cylinder only required a light hone. Assembly, as they say in the technical guides, is the reverse of dis-assembly, so all new GM seals and gaskets were used and a freshly rebuilt head was torqued into place.
Meanwhile, the M62 supercharger had issues as well- the rotors were scratched up as if the engine ingested something. We sent some photos of the scratches to Magnuson Superchargers, so they could provide an opinion. They suggested that the rotors were indeed damaged, and could also be incorrectly timed to each other. The supercharger was shipped off to them to let a 'calibrated eyeball' inspect and rebuilt if necessary.
We will hear back from Magnuson shortly and then install all of it back into the Atom. We'll keep you updated!