hey matthewread
i will tell you that jetpros are a very good performing pipe but a disaster to fit.i bought mine new from hobbythek and they arent the best at all.
im going to help you out as follows as best i can.
1/ pipe doesn't line up with engine if you line it up to side plate or vise versa,(see ahead here to 4/ what to do with this)
2/yes some body trimming required but not much,if you go back along my thread (fg beetle rebuild) and look at the pics you will see.
3/ideally what you should do is mount pipe to engine securely and measure up for a new mounting bracket at side plate to be made up from you local fabricator.
4/ other option is run your bolts in to all fastning points at the same time,whilst keeping side place bolt loose finish in to engine,but make sure you have a start made in to side plate before you fasten head bolts as it will get tight,now this should work but will be very tight,you will have to apply the right torque to head bolts or it will blow out like you say happened.
5/
i just hope now that you havnt damaged your head bolt threads as you say its pulling it out from engine,any pics?
6/ very little trimming required for shell,it is physically possible to mount pipe with out trimming shell if you raise your body mount at the rear but the body does end up a little off..so maybe is better to trim it a little.
is the pipe silenced or not? good performing pipe though just a pain to fit at the start..
some pics would be great to see whats going on,maybe we could offer you more help then.