here is the way to REALLY fix this problem, or you can run into it multiple more times, or just ruin your day when your trying to put it together sunday afternoon and u gotta goto work with it monday morning...... I'm the type of person, if I work on it and take the time, I'm gonna do it right.......
since your removing your old y pipe and replacing it with a new y pipe.....
cut off old stock y pipe just after the exhaust manifold connection, cut off the 2 bolts on the catback connection..... remove from there, remove oxygen sensor wires.....
pull off old y pipe, throw away everything so far.....
remove exhaust manifolds from heads and put them on a table/bench/ground whatever your preferred working surface.....
now you have two options at this point
A)probably best option
find some used exhaust manifolds that aren't rusted to shit with bad studs on them, and replace your old ones with these, install new y pipe, install new hardware, have a happy time removing your y-pipe from now on and its never a pain in the ass....
Believe it or not, all the manifold studs, nuts, and manifold to head nuts on my old 3.0 engine look brand new and shiney, come right on and off... I boxed all that stuff up for a rainy day.... so its not hard to find good used stuff if you look around....
B)Cheaper, more work option
remove old studs, with torch try to get them out, if they snap off, oh well..... get out drill, and I'm not a fan of ezouts, sure they sometimes work, and sometimes they break off inside, and they are harder then drill bits, good luck getting it out at that point
so if you removed the studs successfully, inspect the threads inside the manifolds, repair if nessecary, replace with a new stud/nut set......
if you have to drill it out, repair the threads, insert new hardware, on down the road you go.....
reason why I tell you to remove the exhaust manifolds is, because at this point it is 100x easier to work on them with them off... it really isn't that hard to take off the manifolds.... especially if you have to drill anything, and its a lot easier with torches working on it with the manifolds off the car.....