Hi Tpeti. I've read your stuff on the VFR on BikersOracle.
Your pic looks OK to me. In it you are not exactly level with the top of the head. If you were the exhaust cog mark on the right would be below the top of the head by about the same amount as the inlet mark is above it. In other words the cogs both need to move clockwise by a fraction to have the two marks level with the edge of the head, showing they are timed to each other correctly. It looks to me as if you have stopped turning the crank a fraction too early and before TDC. That's IMHO anyway.
Re. how to reassemble, I would definitely zip tie the chain to the cogs and follow the other advice in post #42 on page 3 above. It worked for me. Note the comments about the error in the WSM for the cover bolt torque.
Anyone else got a comment?