"Only 2 chambers ain’t perfect aligned so I think if the hand was longer, the timing would be bad with all the others. "

That is true, and then what you would do is carefully dress down the ratchet slightly on those 4 cylinders to get your fit.

"Half the time, the timing is perfect with all the 6 chambers and every now and then isn’t perfect with 2 chambers"

That said there can be the issue of the hand having to much play in the frame slot. In such a case carefully peening only the outside of the slot or shimming the outside of the hand might help. Shimming can be done by soft soldering proper thickness shim stock to the hand, and trimming it to profile the hand. You want the hand to push on the ratchet as near center as possible.