Regarding STB power, you can use one of the other functions - TV power, amplifier power for example. With only two IR blaster supported on the device, you can't have them all. Follow the instruction on the remote control setup wizard. You can, for example, on the first page of the wizard, uncheck all except "Amplifier Power" and "Set-top Box Numbers", and then follow the wizard to setup these.
Copying recordings from the PVR seems to make little sense. I believe you can do it though. You probably will have to do some operations "manually". You can for example, run the channel "Composite Hauppauge HD PVR Capture device" (or SVideo, or YRYBY, depending on your setup), and then manually play the recordings from your PVR. That way, you can either watch or (re-)record in MC.