UPDATE: For anyone that cares. I took the exhaust off to get it going for a bit and then slipped it on and bolted it up while running. Now it runs fines, still don't know why it was giving me trouble initially.
Going to test this a couple more times before I weld it up.
Doesn't make much sense but I guess as long as it's working now, run it LOL. Make sure to check the plug and see that it's not running lean with the new pipe.