After looking at the video closer, you have broken motor mounts. Check that out. That will change the belt deflection. Engine should never move that much!!!!!
Can you do this without removing the complete secondary clutch? [It's stuck on the shaft].What size main jets are in it? It can make those flats slides bog. Have you had the secondary apart? Almost sounds like the secondary cover was not twisted when the cover was re installed. Taking off in second gear. Take the secondary off and be sure the cover was twisted and then pushed down and the nuts put on the cover.
I'm thinking you have motor mount issues. See if you can move the engine around by hand with it off of coarse. Watch the video, that engine should never move that much. You have way too much belt deflection, (Loose belt) and when you mash the throttle the engine comes back farther, making things even worse. I bet it runs great once it gets going. Check all four mounts. Use a pry bar and see it the rubber has separated from the mount. It will be hard to see as it will break under the mount and bolt.I can't get my secondary off. I do show it operating with the clutch covesr off in the videos above... seems like it is working, I can push/twist it inwards and it springs back.