When you put the head cover back on, be sure to back out the tappet adjusters all the way AND tie back the tappets. Typically you can loop a rubber band over the intake tappet, out the inspection hole, thru the exhaust inspection hole and over the exhaust tappet. Affixing a head cover on a 500/550 with the tappets flopping around is just begging to bend something.
As for cam timing, cyl #1&4 at TDC, notch in cam shaft at 3 o'clock, (or 9 o'clock). These engines use a wasted spark ignition, so you it doesn't much matter.