The stock gaskets are conical in shape, so wedge themselves in there pretty tightly. You'll likely have to use a small bladed screwdriver to pry them out and ensure the mating surface is clean and free of old gasket material. Right now, by bet is that you've got the old gaskets sitting in the ports. RH furnishes decent (SE type) gaskets with the pipes, and they will work fine if installed and tightened down properly, and evenly.
Working on exhaust systems is never fun, but just be methodical and you'll get it all lined up properly. I would recommend high temp silicone when you slip the mufflers on the head pipes (it's red in color), and tighten the chit out of the muffler clamps...but don't strip them. Also, make sure the clamps are in the right place, which would be about as far towards the head pipe as is possible. They won't slip back on you if you follow those procedures.
If you've got those thingies that lie to the ECM and make the ratio 14.2, it should run fine, but if it was me, I'd get a tuning device on it and have it dynoed for decent fuel economy at cruising RPM's, and drivability, rather than trying to squeeze every last HP/TQ number out of it.