I don’t want to make you paranoid, but if you think you’ve done the valves on the wrong stroke, you could end up with bent valves. I had this on a CB500T. PO bent one.
I’d be tempted in your case to get the rocker cover off, then you would see when all four valves ( is it 4 valve?) lobes are facing away from the springs when aligned with the mark. You could then set the clearances correctly and then you’d be back to a good point.