You need three tools to do this: the "GP3 CMagic", the "Magic Data file creator" and the "Track Editor".
First of all you need to know that some informations used by tracks (e.g. the IA pit stop strategy) must be stored in external files, and can be edited by using the Magic Data File Creator.
You have to extract the magic data (.md file) from your track (.dat file) with GP3 Magic.
Then you need to use the track editor to decrease the race lenght (I use 33% of the total) and save the track. Note that this procedure will destroy all magic data inside the .dat (the track itself) file. Fortunately you have followed my instructions and you have the .md file safely stored
Now you can edit the magic data by using Magic Data File Creator. Adjust the pit stop strategy (note that it is possible to set a probability of cars do one, two or three pitstops), and you need to determine all pitstops windows (the initial lap and the amount os laps in the window). Don't forget to save the file after editing.
After this you can insert the magic file into the track by using GP3 CMagic.
Have fun.