Meow
Andrew that stuff gets baked on with road debris making it difficult to remove.Hit it with PB Blaster or equivalent penetrant and let it sit for a few hours or overnight and add heat if you can with a tap of a rubber mallet it should free up.Keep all components loose ,including headers,use copper paste at connections and all should be well.It's tight but it should go back together without too much drama.
Do you have a PCIII to adjust fuel with the new parts?Also was running well and tuned before changing parts?You may want to at least reset TPS and balance TB's after.
mznyc's post in V11 Sport fitting Mistral Exhaust was marked as the answer