I experienced issue #2 as well on power39. I had VDD1 & VDD2 set to 1 in my /etc/pmconfig. With the stock kernel I was able to boot and run with better battery performance with those settings.

After upgrading kernel to power42 I disabled vdd2 in /etc/pmconfig but enabled it in the kernel config file I set as default (using stock voltage settings , overclocked to 750Mhz, my N900 without smartfeflex was never stable above 750). In my opinion I have experienced stable performance with good battery life based on my daily use (email checked every 30 minutes, music during commute 40 minutes each way, intermittent calls etc).Don't ask me to quantify with numbers.

Do you have battery-graph installed?
If so it would be worth printing out a graph for a day/week with and without smartreflex enabled.
This would give a fairly quantifiable identification of the difference between the 2 states.

ignore nice load means that the CPU frequency scaler will not include low priority tasks in its calculations to determine whether to speed up the cpu or not.

This might or might not save power, usually it's more efficient to go to fastest cpu speed so that a job finishes faster and the cpu can more quickly go back to sleeping at 0MHz.