You only need to disconnect the ground.
Heres the thing with a SC Raptor, the circulator pump for the HE and intercooler runs automatically when the key is on to run position.
That pump draws quite a few amps, and if your battery is low to begain with, you get what I'm saying.
Even with the X4 I've run into glitches.
The only way I successfully got the Tune installed right was hooking up a battery tender, then flash back to stock and disconnect the battery for 15 mins.
Then reattach the ground, hook up the battery tender and flash the SC Tune and then disconnect the battery again.
Make sure no electrical stuff is on, nothing! Make sure your alarm won't set!!!
I've also gone as far as to remove the Tune from the SCT device and reloaded it, just so it gets formated to the latest update from SCT.
These are some of the basic troubleshooting schemes you would do if you called SCT for tech support.
The first few 50 miles is also key, you need to set the drive cycle, best I found so far is to drive reasonable.
Get some street driving in and then go do three decels on the highway or a street where you can decel from 70 to 60 down to 40 to 30 with no braking just let it coast as long as possible.
You don't want to let it just idle forever but it takes about 3 to 5 mins to start the setting the long fuel TRIMS. I usually give a little bump in gas now and then up to 1,500 rpms to get the fuel TRIMS learning.
An good OBD11 scanner comes in handy for watching things progress.
If you don't get 50 miles in the first day don't worry an 8 hr. Vehicle clock shut down is also required.
Once you check that all sensors are ready. Then you can play.
Now you don't need to do all of this but it will take a lot longer to get the PCM to finish all the testing and get a ready status.