I had some cosmetic issues as well. Thanks for all the info/help roostr but if you're going to be doing re-cuts then I would like one also. Screw holes aren't a big deal because they'll be covered with hardware, but the indicator lights are gonna bug the **** outta me. I'm a bit OCD when it comes to that kinda stuff. I know you didn't personally cause these defects and I hope this doesn't put much strain on you, but I can't help that it bugs me. I don't know much about laser cutting, and I've tried to research it but haven't been able to come up with much about the staining/scratching/residuals that I have present.
From what I understand slag or dross is an effect on the edge where heat builds up along the cut (or the HAZ - heat affected zone) and creates a build-up of molten steel right at the edge, which is then chipped, sanded, or buffed away. The issues I have don't seem to be that... and in my research this is more of an issue with plasma cutting. All the examples of laser cutting that I saw were flawless on the front side with some residual affect on the back.
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That being said I do want to make the solution as easy as possible... What about a re-grain? Was that too expensive or were you just set on a coated steel? I wonder if it's possible to do a DIY regrain using a DA Sander or bench-top grinder/buffing wheel and some sandpaper... Thoughts? I'm not hung up on the coating, I have a pretty sick garage setup and could hit it with a 2-part clear afterwards. Damn those indicator lights!!
The stuff you're seeing is something you'll also see when torch cutting; the solution is to blast oxygen or an inert gas at high pressure while cutting to prevent it from settling on the thing you're cutting. A diamond stone on a dremel would probably remove most of this.
Being one of the few people with multiple plates in their possession, I'm ALSO seeing a pretty high variance in the switch cut locations from plate to plate; not enough to prevent me from lining switches up with the PCB (I THINK...I only have one finished keyboard. Time will tell...) I was able to make the bad plate work for the mounting holes using a very good floor standing drill press and high speed steel bits...
Plate quality is a bit of a let down for me.
With regards to thickness, I've cut the standoffs/spacers off all of my teensy boards (not easy!) and as a result I'm able to get the teensy boards super close to the Phantom PCB; since I'm putting in USB breakout boards (from Sparkfun) I'm making my own interconnect cables to go from the teensy to the breakout board. In the end, 1/2" standoffs are easily enough clearance. In the front, I can even go shorter.
On an aside...turns out I think MX Clear switches are terrible. Ordered replacement springs from MK along with some Teflon lube.