Wowzers.
I just found a guide (It was at the top of the PT forum thread. I don't know why i didn't see it last time i looked. ) written by Taugrimm that is fantastic. If anybody come in to this thread with similar questions,
http://www.swtor.com/community/showthread.php?t=154123
head there and read up. Also great for Vanguard troopers.
If anybody knows of an equivalent, hell even close, guide for Mercs please post it.
Sully