After seeing the second batch of photos of the flanges I’d like to retract my comment on “hand twisting” them straight.
All though my Land Cruiser experience is limited I’m a retired pipefitter after 45yrs and am very familiar with weld pipe fabrication and the effects of weld heat pulling, pushing, and warping fabrications in all sorts of directions. Even with the perfect jig setup, when the fabrication is released from the jig it can react to stresses put in from the welding and distort out of shape. The jig may be perfect but the human welder is often inconsistent. One welder may put one, two or four tacks on each pipe. Another welder might tack the outside pipes and work inward. Or vice versa. And the same goes for welding it out. Then throw in coffee and lunch breaks in the middle of the weld out and who knows what will happen when it’s released from the jig. But I guess how it happened doesn’t really matter. Yours is out of whack! So if SOR doesn’t replace it with one that’s true, I would (before machining) attempt to cold bend it back to true as possible. I would start with maybe C-clamping or bolting it down to a flat surface like a welding table or a section of stout steel and get a feel for how much force it takes to flatten it out. If it takes more force then you feel comfortable with then you could add spacers (flat washers) to the opposite side and over flex it, bending it in the right direction. With patience I think you could get it close to perfect and may minimize or eliminate machining. Sorry for the long post.