Welcome to the SeeMeCNC Community

I guess I'd like to have a little bit more control over the PID tuning, instead of relying on the Autotune script, to optimize the heating of the hotend and bed.

Could anyone direct me towards a good way to do some temperature data exporting/logging?

Rostock Max v2
0.91 Repetior Firmware (loaded via Arduino 1.6.1)
MatterControl 1.4
Windows 7 via USB

Repertier Host has temp data logging built in:

http://forum.seemecnc.com/viewtopic.php ... 4&start=25

It displays current temp/temp setpoint and power output for both Bed and Nozzle though the link above I've only got bed temps displaying.

Repetier host like RocketMagnet said. I usually go with P value from PID auto tuning, or very close, but I and D are miles off. all my I and D values always end up less than 1.