3 options, best to worst.
1) Grind down welds. Use stock nuts.
2) Buy smaller nuts and same size washers. Snip crescent out of washer to seal around the weld bead.
3) Buy smaller nuts and no washers.

Also on your to-do list. Check for anywhere that there are signs of carbon buildup. This will be your exhaust leak. Check the EGR nut, check O2 sensors. Check the 2 flanges. Find out if there is a mystery hole that I didn't see somewhere between the pipes.
-Jeff