Ok, now I am confused. I was going to answer your questions but I think we will just end up going back and forth and you will be more confused. Are you learning or have you learnt time series ? Because some of this stuff is pretty fundamental. Think if you are struggling with this sort of stuff maybe it'd be better to pick up a time series book and start from the beginning ? Here's a link to some stuff on pairs trading I've seen before on the web and covers the basics, but again it may confuse you.
http://www.yats.com/doc/cointegration-en.pdfBut with some of the fundamental questions maybe get a time series book ? Hamilton is pretty severe but I think there are some more introductory time series books out there. Not sure what's online but am sure there's stuff there as well. btw, I kind of did the same thing a few years ago when I starting analyzing market data. Jump in and apply techniques, thinking I did it right, but I was doing it wrong. Everyone who told me otherwise was just being stupid and pedantic. I didn't need all that introductory stuff, I was smart so I could just jump on to the super sexy advanced techniques. I had to spend alot of time going back and understanding all the fundamentals and now I think I am starting to do it right, but still have a lot to learn. The more I learn the more I realise I don't know, so don't take offence when people give you advice, there's probably something in what they are saying and maybe you don't get it straightaway. I often have to go back to high school books on some topics to get the basics correct. At the same time on the internet everyone with its general anonymity seems to be an expert, so what's important is you listen to the advice, do your own analysis and find what works and doesn't. I was just trying to steer you in the right direction. Try to find data sets outside of finance to work with as well, as looking at different data sets may help your understanding.