I just freshened my big block after 100+ passes and I had the lifter shrouds facing the block not the valley. I just put it back together the same way. Do I need to pull it apart to change them? There is plenty of clearance the way they are in now and everything looked fine from the last 100 passes. Should I pull the intake and switch them around?

If it ran fine before, I don't see why you'd need to change em. Evidently there's plenty of clearance.

Is it just a clearance thing? The lifters had been installed in a engine previously to me buying them and I didn't have any directions. They are crower lifters.

Make sure the pushrods aren't touching the link bars.
With several models of roller lifters in a bb mopar, if you put them in with the link bars facing the valley wall, the link bars can rub on the pushrods. Sometimes to the point where there is hard enough contact where the link bar won't allow the pushrod to properly seat in the pushrod cup.
Obviously I haven't tried every brand of lifter out there, but it wouldn't have been right in the ones I've seen.

Personally, I'd turn them around.

FYI, I think a picture is worth a thousand words.

Wouldn't even be a big deal but I have to order another set of these Mopar stage VI intake gaskets from Mopar. I wish I had a standard head intake combo.

I didn't use anything special for intake gaskets on the motors I put stage vi heads on.

Here's. how you can check to see if the pushrods are contacting the link bars.....
Working with one pair of rockers, turn the motor over so both lobes are on the base circle,
loosen one of the adjuster screws and see if the pushrod can be tipped even closer towards the rocker shaft. If it can, and you're sure the pushrod is properly seated in the lifter, you "should be" good.
I've seen it where the pushrod is touching the link bar, and when the adjuster screw was backed out a bit, the pushrod would slightly "spring" out farther away from the rocker shaft.
Higher rocker ratios aggrivate the situation even more.

With stage vi heads, you might be able to physically see if there is any contact or not.
It's pretty easy to tell with OE heads, not so much with the aftermarket stuff.

The heads and intake have had so much machining done to the mating surfaces that I have been using the Mopar gaskets in the thick version and they have been working good so I think i will just keep using them. They are cheap enough and its easy to pull the intake so I might as well just flip them around so I know they are correct. I inspected them when I had them out and the push rods do have rub marks from the rivet on the cross bar of the lifter but not enough to cause any issues last time. But I think I will just turn them around for a piece of mind.

Good plan !

THIS.........Big blocks are on cam side cos the p-rod angles are a fairly straight shot and Small blocks are against the valley due to the not so good p-rod angles..........