You're partially correct on the logger being incorrect. When reading the logger, it will show you what the ECU sees for the Maf frequency. Since the SAFC is altering the frequency the ECU sees to control fueling, the ECU gets the wrong value and thus so does the logger. Obviously by wrong value I mean the value changed by the AFC settings. Also, if the TPS sensor is messed up, or, not closing all the way, the AFC will not show this. The SAFC learns the TPS values so the minimum it shows will be 0% and the maximum as 100%. Those values will not correspond to the logger all the time. WOT should be the same but at idle, the logger should say 9% I believe and the AFC will display 0%.
As far as what method I would use, I wouldn't settle for less than soldering. You may be able to get things to work with those God-awful vampire taps but you might as well do it right the first time. Make sure you follow the instructions on the grounds because it does matter which is closer to the ECU. You'll see what I mean in the instructions.
After it is installed there are several pages that will walk you through tuning. Good luck.
-Josh