From the set pitstop suggestion thread:

Quote from Scawen :

We can set number of laps and a penalty, so I guess the number of pit stops done is the one missing thing.

I noticed that the PEN packet has a spare byte, could it be used to set custom penalties in addition to predefined ones? e.g. 5s, granularity of byte allows for single second penalties.

These penalties could be easily adjusted, though I must say I'm not sure how it should be presented to the players or actually set as part of the PEN packet - alternatively, add a new packet for this, such as PET (PEnalty Time)?

The command to set the penalty could take the format /penalty USERNAME TIME.