You have a number of issues, but the one that most concerns me is the metal chunks. I can not identify the piece you have pictured, but more pictures would be helpful. By seeing all the pieces we might be able to identify what it is from. Until we can try and identify it all that will happen is that horrible and depressing thoughts will run through our heads.
Briefly, on your other issues:
I would suspect the Dyno Jet kit. These are sometimes set up to be stupid-rich and could cause the chugging problem because the idle mixture is way too rich. The rest of the mixture is way too rich, too, but there is enough airflow to deal with it at a higher RPM.
Do not worry about bits and pieces of a gasket, RTV, etc in the screen. This is common and that is what it is there for. It has caught up 55k miles of crappage from the previous owners' wrenching.
KLR clutches are tough and the best parts to put in them are OEM parts, but they usually last forever. You've done no harm by putting the EBC fibers in, though. Strange that the springs didn't work, but not unheard of. I prefer Barnett or OEM.
If the clutch is at fault on the grabbing it could be that there are grooves worn in the fingers. These can be dressed down, but pictures would be required to see if it is really excessive. You say they don't catch on your finger, which would lead me to believe they are not a problem. I know my clutch hub has some wear, but it doesn't make the clutch grab badly. One of the best mods to the KLR clutch is to install an extended clutch are from Twin Headlight Earnie. Makes the clutch pull easier and increases the friction zone at the lever, improving feel. Put this on the back burner for later. https://www.souperdoo.com/stuff%20th...this-years-ago
Flakes in the oil, or glitter, is usually a sign that the balancer chain is eating the case. Here you need to verify that the flakes are aluminum and not steel. If all or most of the glitter sticks to a magnet then there is something more serious going on. Steel things don't usually turn to glitter or flakes, they show up as larger pieces, such as the one picture. Something goes bang, gets caught up and spit out into the bottom of the engine. Glitter is usually aluminum from a chain wearing on the case, most commonly the balancer chain.
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