Yep---Fire up the torch and start cutting, untill you can at least get the flange (or flanges) bolted to the heads. Be sure to install the proper gaskets (you only want to modify these things once).
--better yet, do your cuts with a cut off wheel or hacksaw, as square to the pipe as you can eyeball it--that way you may be able to just rotate sections of primary tubes and then reweld them back in place.---get as much weld on as you can with everything still bolted up, then let them cool untill they are stone cold before unbolting them and finishing off the welds in the areas that you couldn't get to.