Sevels,
The engine looks like it's running fine. Can't quite see the problem from the video, but if the rim of the flywheel is moving slightly side to side, that shouldn't cause a problem. If it isn't centered on the shaft, that's more serious, but can be fixed by adding some lead weight opposite the eccentricity. I notice your gib keys aren't sticking into the flywheel hub very far. That's how mine were before I did some tweaking (see below). If you ever pull the gib keys, it would be a good idea to take a file to the tapered side and get them to stick into the hub a little farther before you reinstall them. Gives more surface are in contact with the flywheel and should be more secure. After I reinstalled my keys, I had problems with them walking out until I did that.
Andre,
The keyway in the flywheel hub of my Ashwamegh 6/1 was tapered about 0.007"/inch. The keyway in the crankshaft should be flat. I recently fitted my gib keys to the taper using a file and a black sharpie marker to indicate where the contact points were. Took about 1/2 hour for each key, but now I know most of the taper surface is in contact with the flywheel hub keyway.
Halfnuts