Did you remove and install a tranny or just exchage the fluids? I think i misunderstood you to mean you removed and installed a tranny.
Wear eye wear protection!
It's not difficult to remove the exhaust, but the bolts can be stubborn and seized in place.
The hangers can be a bit tricky also. For the hangers, go to your Wal-mart or auto parts store to buy a can of silicone spray. Spray them on the rubber hangers holes where the exhuast mounts to. This makes it easier to slid off and on.
If the exhuast lines up well, then you shouldn't have too much trouble installing the new aftermarket exhaust. If not, you might have to figure out ways to make it work.
To be honest, if I were you and the original bolt have never been touch, I would just take it to a shop to remove and put on the new exhuast. It shouldn't cost you more than $50 dollars. Any exhaust place should be able to do this for you. Better to go to an exhuast place than a general mechanic because they have better welding experience if you need them to make an adapter for you. Plus, the stock exhaust is extremely heavy. There is a possiblity for injury if you don't know what your doing and don't expect it.
Watch him do it and let him replace all the stubborn bolts/nuts with new ones. Then if you need to remove the exhuast in the future, then you can attempt a DIY. Your new aftermarket exhuast won't be as heavy to remove and the bolts won't be stubborn to remove.