UPDATE: Well today we sealed up the leaks in the headers. To seal the Y-pipe we used a nice thick layer of exhaust tape sealer then on top of that we used the summit clamps. As for the down pipe flange we used 2 heavy duty gaskets. When we looked at the old paper gasket it was already cooked (well done). It was a PITA to get the clamps on right with the exhaust tape and we did the best we could.
So far there is absolutely no leak from the flange. From the Y -pipe it was still too early to tell because the tape had not cured on throughly enough. Although the good news is that the car is once again Buick level silent while crusing. We can finally hear the supercharger whine again!