I've done a few now if anyone is my way and needs a hand 
Amego, the last one I did I had turn turn the rubber cap from the passenger side up the other way and it fitted. Are you saying your new matrix doesn't have offset pipe loops on the passenger side end?
You got it in one welung, as well as the pipes not fitting. It would appear you just cant get a new one now for a pre facelift. If you went down the main dealer route without trade card it would cost you in excess of 200 nuggets for the updated version!
The rubber boot on hindsight is not really the problem, MDTM came up with a simple solution

, but you dont know its no good until you put it in and the coolant p*sses out of the pipes!