Aftermarket Y-pipes do not contain the precats and will not resolve the original poster's dilema.
Precats are over $500 each and I have yet to find an aftermarket source for them for the Contour V-6.
My guess is that the codes the dealer pulled were P0420 and/or P0430. There is no sensor after the Y-pipe cat, so it is never checked by the engine's computer for efficiency of operation.
Bummer. Too bad that your car waited until your 8/80 warranty expired.
My suggestion would be to order the pre-cats/exhaust manifolds from a discount Ford parts distributor, then hire a local shop to replace them at the flate rate times.
You can then get an aftermarket y-pipe with its cat to complete the job. Total cost should be around 60% of your oringinal quote.
Steve