Like skid said it looks like something is sprung. In my experience these bulbous 2T pipes and silencers are ALWAYS sprung to some degree. (one of only a very few reasons I'd ever consider a 4T) Can't hardly help but bash them exposed as they are... If you have the stock Messico on there I think they are relatively thin and prone to bending.
The subframe is a mushy piece of aluminum that is also easily bent so I
expect some amount of misalignment every time I pull my silencer or pipe.
None of it is particularly hard to tweak into shape but it takes some ingenuity.
Did you take off the expansion chamber or is that still mounted as it was? A small variation in placement of the outlet from the expansion chamber will make a big diff in where the end of the silencer ends up. With silencer off how does the end of the expansion chamber line up in relation to the subframe, shock, and motor case. (just above the kicker) On my '05 MC 250 the outlet pipe on the expansion chamber is roughly centered between the subframe and the shock. The bottom of the pipe "just" clears the bump in the case above the kicker. If that looks o.k. then...
First approach I'd take is stick the silencer on the end of the exp. chamber and only stick a bolt in the upper (rear) mount on the subframe. You might actually find that a spacer in between the grommet and the subframe is what's needed. Those mounting tabs on the silencer can be whacked around a bit to make things line up too. That goofy bend in the inlet pipe on the silencer can be deceiving.
If that doesn't work what I'd do is take the main pipe off and mount the silencer on the subframe and see where it points to. If it's not pointing in the right place persuade it to do so.
It's hard to tell what's bent when everything is under tension.
