Hey Djack
First of all welcome to the forum, your right Pebbers lessons (theory and guitar) are very good they have helped me a lot in the past year.
Becuase I'm only a member for just a year I will see if I can help you answering your questions.
1) Regarding your question on altered scales I found the following explanation on Wiki : Altered Scales
2) I don't know exactly what they are but I guess these are chord scales that are not built on triads and with alterations as mentioned in the above link. Very interesting question though so if im completly wrong I hope someone will explain this better as I can.
3) I thought that Chord families are chords that below to a certain scale. e.g. Major scale has:
I=Maj II=min III=min IV=Maj V=dom VI=min VII=dom
The above chords is the chord family of the Major scale, thats my understanding. But I dont know where you have seen this because if I take a look to the modules, Module 5 is Eartraining. So I gues you looked at the syllabus there I find lesson 310 which mentiones that there are 5 Chord families.
Although this replies will is not fully complete I still hope it helps you a little bit. Maybe there others who know more about this, to me it seems it are pretty advanced matters.
Grtz Ray