Here's my last 3L project, this 05 Sable motor had 46K I think. So, you really shouldn't have that sludge.
Here is how I prepare heads for porting.
Head, with nothing in the intake port.
Heavy shop towels stuffed down on top of the valves. Very snug. Heavy shop towels required so that you can later remove them with needlenose and they don't rip apart.
Heavy grease packed on top of the shop towels.
Hard to tell in this photo, but the engine is rotated at least 90* so that many shavings fall out of the port. Even then, plenty stay stuck in the grease. I then rotate the motor completely upside down to remove the grease/metal mixture. I will typically start with a large flat-head screwdriver to scoop out the grease/metal mix. 95% of the shavings are kept in the top 2mm of grease, so scraping that layer out with the screwdriver is what I spend a lot of time doing carefully. Then carefully pull the shop towels out (motor still upside down!). Use your fingers and towels to wipe out all bits of metal remaining (there should be virtually none if you were careful enough taking it out.)
It's also a good idea to polish/clean the gasket surface (if need be) before you clean out the ports.
You may also notice that I have the 3L valve covers and 3L timing cover on. I do this because I do not plan to reuse them. Therefore I am less concerned about them staying 'clean'. Do your porting with all openings plugged, even if they are nowhere near the intake ports. And port with the valve covers and timing cover you plan to discard, not the one's you plan to use in your final product. It may not make a difference as you can clean them of with compressed air, but I don't and have had much success.