Just did -9's on mine and we ran in to the same problem.
You can either go out and get a pair of drains like what GCG sell: http://www.gcg.com.au/index.php?page=shop.product_details&flypage=flypage.tpl&product_id=209&category_id=131&option=com_virtuemart&Itemid=101
Or just bend the pipe slightly (and slowly), which is the option we chose: Mounted the flange the best we could then used a breaker bar handle down the hole to lever it away from the bolt head, worked well - just bent it a little, checked it, bent a bit more, checked it, etc.
Another thing to double check is the compressor housings are rotated around in the correct position, because mine was slightly out, ie: rotated a bit too much clockwise. This didn't become apparent until I went to install the 'twin turbo' pipe and the rear turbo outlet flange didn't mate up, so had to get a longer silicone hose from the rear turbo to the TT pipe.
So I advise just quickly comparing them with the ones you pulled off and adjust if necessary.