Yes, the rockers are on correctly and the pushrods seated in the little dents like they are supposed to.
If "all of a sudden" you have half your pushrods not seated in the dimple on the rocker arms, then my first guess is that one of them isn't really seated or maybe a rocker arm is slightly hanging up on one of the rocker arm shaft pedastles (sp?) when you bolt up the rocker arm shaft or maybe the bottom of one of the pushrods is on the "lip" of the lifter and not down in the lifter's dimple. All pushrods should be at least snug and some super tight (because those valves are open). I suggest you take a REALLY good look under the valve covers for more bolts & maybe go "fishing" again with those magnets for more stray parts and take a good look to see if something "looks crooked". You're idea of cranking the engine over with the valve cover (or covers) off isn't a bad idea. Look and listen carefully to help you narrow down (front/back or left/right) which cylinder(s) is affected. You can just unplug the plug wire coming out of the ignition coil.
To check pushrods for being bent, once you clean them off pretty well & make sure there's no sludge on the sides, they should roll smoothly on a mirror. If one is bent & doesn't roll straight, replace that one.
I suggest you leave all the pushrods/rocker arms/etc. in the same position they started in if possible (don't mix-n-match if you can help it). I suggest you keep the pushrods facing the same direction up/down too. On each rocker arm/pushrod/lifter combo, you can check for excessive wear on the end of a pushrod or in the dimple of a rocker arm vs. the other ones on the motor. If everything looks straight & moves normally, the last thing to check would be a "collapsed lifter". Lifters have springs inside & that is part of what makes each pushrod fit "snuggly". If one of those springs breaks, that pushrod will "seem too short" and fit really loosely.
One last thing...and only if you changed valve covers...look underneath them to see if some metal looks "shiny" or dented like a rocker arm was hitting it there. When you change stuff, sometimes the rocker arms can hit the valve covers. That's why the other guys are asking if you have baffles under your valve covers which would stick down a little bit.
And you need to use a torque wrench when you bolt up those rocker arm shafts. The bolts might "feel" tightened the same, but you can get fooled really easily by the valve springs... a torque wrench is a must. You can also use a little bit of silicone "RTV" gasket sealer to hold the valve cover gasket in place while you're putting it back on. They can slip over a little bit sometimes and leak like crazy...we've all had that happen at least once.
