Hi Anfos,
I just purchased my brand new Triton MN11 GLX-R in December last year and it came with the factory sports canopy from Mitsubishi and you wouldn't believe it but I too have had nothing but trouble with allignment and the rear door not closing properly.
The first canopy was replaced only weeks after I picked it up because the actual mould was not correct. The door wouldn't close, the tail gate was just about hitting the canopy door, the gaps on both sides were unbelievable and the door was extremely hard to close, it wouldn't lock on the LHS!!!
Anyhow this was replaced but the 2nd one then leaked like a siv!! The gap down the RHS between the canopy body and glass door was huge but Mitsubishi said there was nothing they could do to correct this. To stop the water leak I was told it needed the weather seal kit fitted, this was an extra cost (can you believe it), and it wasn't until I drove off about half an hour later I noticed two huge chips down the LHS between the canopy body and the cab NOT HAPPY!!
I took it back to the Mitsubishi dealer again and this time it had to be resprayed, off the road for another 3 days!
Anyway this has all been resolved and touch wood I won't have any more problems with the canopy.
I wrote a nasty email to Mitsubishi in Adelaide explaining my entire frustrations but that is where it all ended!
So Anfos you are not alone on this one, it has not been a good start for me. As for the vehicle I couldn't be any happier, I now just have a huge wish list on what mods I want to do but I just don't know where to begin, tattslotto would be a good start.