With that amount of metal in just the valve covers and also some in the filter, I recommend tearing the whole engine down to flush out the block. I know it's not what you want to hear but small flakes especially found in the filter will eventually cause damage to bearings. Metal should never be in oil. Remember that the oil galleries probably have metal too. It will eat bearings, journals, etc over time.
​​A quick fix won't work.

 

update for anyone curious
started tearing down the top end yesterday, valley, rockers, and gave it a good look-over so i could do the stem seal/retainer/spring install today
got about halfway through and the rope i was using tied itself and is stuck inside the spark plug hole, so its time to pull the heads, at least I'll get to clean it out a bit more, the guy that had it before me didn't give too much of a damn about it and never, ever emptied the catch can. those intake ports were BLACK.
took out the pushrods and noticed one had a decent amount of flakes on it, but they all looked alright, and to my surprise there was one rocker with the trunnion bolted to the rocker tray backwards, leaving a light imprint on in, but really not that bad luckily, there is only 20k on this motor.
on cylinder one it looked like there was no valve seal at all, there were a couple metal rings which i assume used to be seals, and the metal seats.
im no expert mechanic, but after watching almost every video on YT about taking off the heads, it seems really do-able, any advice is appreciated. will give some updates tomorrow later in the day if everything goes well, a little earlier if not

 

If you're pulling the heads then my advice is to have them checked out. If you can swing ARP hardware that would be my suggestion also in order to get away from the stock TTY bolts. Those are a one time use but I'm sure somebody will chime in and say otherwise.

 

if i had the time to i would, its my daily and im taking off of work to fix this situation, if nothing else there is a pretty reputable speed shop nearby i could waddle over to and have them check them out.

 

I'd hate for you to go through all that trouble only to have to do it all over again due to worn valve guides. You should at least check and make sure that you do not have excesive movement of the valves.

 

good to know, is there any other main areas of concern? i`ll be looking everything over pretty closely, lifters etc.
say all the lifters still roll easily with no hiccups or play, do you think if would be safe to pop them back in the tray and keep running them, or should i look for some new ones, same with the tray, is that an need to replace item?