Good news! I rechecked the leakdown today and it seems the previous poor result was due to contamination in the valves. Cylinder 4 read 2%, same as last time, and 6 read 3%, vs 8% last time. So the engine is just fine. Whew!
I also have another interesting data point to contribute. These numbers were measured with an aircraft style leakdown tester:
Eastern Technology Corporation
I like these aircraft testers because unlike the automotive ones, their calibration is specified -- the measurements are relative to a .040" orifice at 80psi.
So today I measured these two cylinders with a Snap-on tester after measuring with my aircraft gauge. The Snap-on read 3x the leakage percentage of the aircraft gauge, so it indicated 6% and 8%. Nothing wrong with either reading, just different calibration.
To my knowledge there is no standard calibration for automotive leakdown gauges, so different gauges will read different percentages for the same amount of leakage. However, the 3x factor that I measured today gives one data point for calibration of the Snap-on gauge.
-Juan