Update:
So, after getting the wheels taken back off, the "waa waa" sound after the lift, I did a little bit of investigating. My assumption for this:
That the stock height measurements for 5th gen 2010-2013 models will be within 1/4" +/- for error - so I have been using roktoy's stock height measurements - with my post earlier, this gave me after install ~4" of lift up front and ~2" out back.
With that - I went back and measured from the bottom thread of the COs to the bottom of the bottom disc. This measured to 1.25" - doing the conversion from TT's instructions with 1/4" = 1/2" lift - this gets me to the 2.5" lift that I requested from TT when I ordered the BOSS COs. However - I would think/assume that the measurement should be take from the bottom thread of the COs to the TOP of the bottom disc as this is where it comes into contact with the top disc which controls the actual height from the CO. The disc itself is 1/2" thick - which would equate to 1" lift - thus, the whole lift would be ~3 1/2".
IF that is not correct, and the measurement should be take from the top of the second disc (the one in contact with the spring), then just add another inch of lift, and the total lift would then be 4 1/2" of lift - which seems to be closer to what everyone is experiencing (at least in this thread).
So with those assumptions, I went and adjusted accordingly, and my measurements are not sitting as follows:
DF: 37.75
PF: 38.25
DR: 39.25
PR: 39.25
The "waa waa" has gone away, and the boots look much more relaxed (although I still think the inner boot - closer to the drive train - seems squished in, probably still gonna stretch that one about 1/4"), and I have a my "normal" rake back. I've got close to 500 miles on the new set up - gonna remeasure everything this weekend, and then take it in for a "final" alignment.
Hope this helps or provides some good discussion - the only other thing that I can think of is that the 1/4" = 1/2" lift is a bit off.
Trail on~