That timing may not be what's at the crank. There are corrections for boost and IAT. The correction table can hold negative numbers to subtract timing as temp warms up. Positive numbers will be added. Also, some of the vacuum related parameters might need to be changed manually during a 3 bar conversion... make sure those are done.
Hard to tell what's happening without seeing a log file and watching over time. Being able to see the values as they occur is worth a bunch.
You know that knock counts don't always start at zero with $59, right? The ecm is looking for change over time. Changing counts without KS activity is a code issue and doesn't indicate real knock.
Nice find on the Camira bin! I'll have to spend some time studying that one.