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(well second hand) exhaust for my car and when attempting to fit it hit trouble. At this point I decided to take it to an exhaust place to see what their opinion was. They say in order to fit it they'll have to cut off both flanges on the cat and the exhaust and weld a pipe between to bridge the gap. If the metal has rusted away, (as Toyota exhaust flanges normally do), then welding new metal in is the only answer. This would make the exhaust and cat one piece, I'm surprised I haven't read about others having this problem before Heat may work, but they may be well past that stage. Try shopping around. Also, the guy is trying to do a "proper job" remaking your flanges. One reason why old OEM exhausts systems don't fetch much s/h. this would mean the systems was 2 peices still at least. How badly rusted does the flange need to be before it's un-useable? Its a pricej job to wled new ones in, more than a 2nd hand exhaust is worth for sure.'real' metal ofter the rust has flaken off is even less, its almost like the pastry on a sausage roll, when i changed a mates std exhaust to a stainless his was so bad he needed a new downpipe and cat just to change the back box£££ for it...will be your best £ for £ option in my opinion 
,,alternately these will do the job ? They have surface rust but until i start to cut it apart I wont know how badly rusted they are. The garage said they're probably not okay but I don't think he anted to say for definate. (This seems like the tidiest solution and I dont see why it would cost more than option b) I'm swaying more towards replacing the flange becuase I'd still be able to change the exhaust if it was too loud or didn't look right etc. Whats peoples thoughts on what this should cost?