FRPP is in the process of redesigning the Pro-Cal tool.
When you order the Pro-Cal tool you will specify your computer code taken from the sticker on the case, tire circumference, gear ratio, and fuel octane (91 or 93 only). As of now, this information is used to make the one premium tune you get.
The tool is only meant to be used with one of their parts such as cold air kit, drag pack, or supercharger kit.
The next generation pro-cal tool is hopefully going to offer things like tire size/axle ratio adjustment and other minor parameters. It will not offer any end-user tuning parameters such as fuel or spark.
As stated by others, it is much better to go with a Predator or SCT that has pre-loaded tunes for many cold air kits and can accept custom tuning, data log, and also allow you, the end user, many parameters to adjust on your own.