1" raised engine mnts .........quite common on YJs and TJs to get drive shaft angle correct...........Might work in your situation
Send the photos to Headman and ask for their suggestions with the thinly veiled query of WTF is wrong here?
personally i wouldn't dimple the headers, i have seen oval downpipes to cure clearence issues but making round into oval is not nessesary an easy option.if you want to take the header route mark the area remove the header and slowly squash the header in a press just enough to give adequate clearance, unfortunately this is a one way fix for the situationormark the chassis rail where they foul and then with your cutting and welding skills scallop the area to give clearance. take into account sideways rotation and forward aft potential movement to gauge how much to remove. Add an additional brace to the top and underside around the scalloped area to boost the strength back.
What a joke, imagine if you were told the same thing when your car came backfrom the panel beaters and the door didn't close