well the alternator was fine....

I got a new one and a new battery, but the reason I was having bogging issues was because the main connector that goes to the alternator was not connected all the way and I was just running on the battery.

When I would accelerate rapidly, the voltage would drop to like 9 and the battery would not supply enough voltage to keep up.

I have not put the cat back on to see if the exhaust is indeed clogged some how, but I am assuming that it will be fine. But I have to drill out 2 of the studs on the cat as I broke both taking it off.