If there's dirt on the inside of the filter then thats definitely your problem and you'll keep chewing through top ends untill you find where it's coming from.
As has been mentioned make sure you run your finger around the edge of the filter to make sure it's seated right, i'm guessing thats your problem. Also check where the boot meets the air box and silicone it to make sure.
I have a Loudmouth intake, it is pretty hard to mess up installing those air filters. When I did use the stock cage, I only had a problem once with the filter not being seated right, after that I triple checked every time I changed filters.
First off, welcoem to the forum! Secondly, I completely understand how frsutrated you must be and you're completely right, this is ridiculous, but stick with the smart dudes on here, me not included, and it'll get fixed.
What was the reason for swapping out a piston at 5 hours? You should get ten times that out of a well tuned 250. Have you got pictures of the old pistons? Also if you could post up a picture of your sparkplug's action end, that would speed the process too. AS for the dirt in the airboot, is the 2012 250sx equipped with the no tools air box cover? Pretty sure it was introduced in 2011. Make sure that is properly clipped in because I've found that mine (2013 250SX) can look and feel like its clipped in but the bottom clip is off. Also, have you changed the jetting? Have you noticed any odd noises coming from the motor?
Again, bear with it and it'll get solved one way or another. The air boot problem and piston problem are possibly two separate problems.
Thanks, at 5 hours I had no compression and the bike wouldn't even start, so I did the top end. I could get pictures of my old pistons I have one from the 250 and one from the 300 kit. I haven't changed the jetting and I haven't noticed any odd noises from the motor.