Metal shavings in the filter is relatively common, happened to both my YZFs when new. If this persists w/ frequent changes you could have problems, but I wouldn't worry about yet.
If you drain both the tank and engine and replace the filter you should put in 1,600 mL, or about 1.7 US qts.
If you want you can reuse the stock oil filter, just carefully back-flush it with something (cleaner, solvent, diesel) to remove the debris. OTOH I think a replacement is less than $10...
And yes you drained the oil properly, another trick is to tilt the bike over slightly (to the right) and remove the lower oil filter cover bolt first, allowing the oil to drain out. If there is junk in the filter make sure you clean it out of the filter housing also.
I would also recommend a magnetic drain plug (in the motor).
Hope this helps.