Chris, in your logging program in histograms pid #1 should be Main Spark-Timing advance, you can easly see what your timing is at part throttle to wot. Pid #2 shows knock retard, meaning if any timing was needed to be pulled (good way to see if ya need to pull any timing). You can also see your timing value in the chart Display if it is a parameter you use to log.
Here's how to eliminate kr. If you see any kr in your histogram follow this. Say you have 4* in cell (4.0, .20). This should be 0, so subtract 4 from VCM editor>edit>Engine>Spark advance>main spark vs Airflow vs RPM open throttle/moving>high octane (4000, .20) cell. Just subtract by clicking the plus selection (after selecting/highlighting box) after typing in -4. Do this for all corresponding areas with KR. Log again and varify that kr is gone. Hope this makes sense, but am sure once you get to the areas you'll figure it out.

There you can also log duty cycle if you have chose it (injectors big enough). The help files are really good on getting your logging parameters set-up for what you like.

For a/f, also in histogram and chart display, you'll see it in narrow band (stock), but narrow band will not be as accurate as a wb the farther you get from 14.7:1 ratio. But will work in a pinch, to get a basic idea where your at.
here's the numbers to base opinion on .880-.890 is ideal for n/a, lower numbers are leaner ie: .800, and higher are richer ie: .900. Now I don't know what a corresponding number represents (in my notes somewhere) in actual a/f, but someone reading along may have the break down. I allways have used a wb, so...
Hope this helps to get started, as HPt can be quite a learning process. If I didn't make sense somewhere let me know.
Robert