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A common issue with most 3D printers is maintaining print bed flatness. Aside from adjusting the flatness with the four corner thumb screws, planarity is also critical. Print bed warpage is hard to correct, and that's one reason why some people mod their printers with glass beds (not to mention adhesion issues).

I performed that mod on my Mega since I had some flatness issues, and I wanted to use smaller nozzles, which required critical flatness (thanks BETLOG for the heads up!). What I found was interesting so I thought I would share my experience.
I ended up buying this glass and thermal pad:
https://www.amazon.com/gp/aw/d/B01LFOI2VS/ref=mp_s_a_1_2?ie=UTF8&qid=1500224214&sr=8-2&pi=AC_SX236_SY340_QL65&keywords=print+bed+glass+220mm+220mm&dpPl=1&dpID=41A4G4c6IHL&ref=plSrch
https://www.amazon.com/gp/aw/d/B06XX7ZMN7/ref=yo_ii_img?ie=UTF8&psc=1

However, after installing it and performing the flatness adjustment, it too seemed just as warped as the original aluminum bed. I could get all four corners adjusted perfectly, but the center was almost .2mm higher. What gives? Some people were reporting that their glass was coming in warped from the supplier, so I checked mine with an accurate straight edge and it was dead on flat, so where is the warpage coming from? I thought maybe the paper clips I used to hold down the glass was warping it, but I also checked it installed and it showed perfect flatness, so how is the center rising up .2mm?

As it turns out, there was a bend in the two y-axis shafts, which I found odd since they are made from high precision steel. Well what I discovered was the shafts on their own were pretty straight (after removing them), but what was causing them to bow were the end mounts. The end mounts don't have a very large mounting surface so they can easily tilt if there are any surface variations in the sheet metal cover that they are mounted to, and in fact, they mount very close to the edge where there is a bend radius. You can tell if the alignment of the end mounts are off by loosening the four set screws (one on each side of both ends) and attempting to slide the shaft back and forth. If everything is aligned well, they should easily slide and rotate. Mine didn't. What I did to fix the problem was loosen the end mount attachment fasteners (to get the jammed shafts to slide out) and take a 5/16th drill bit (slightly smaller than the shaft diameter) and insert the smooth end into the end mount hole. Carefully use the drill bit to bend the sheet metal slightly, correcting the tilt. It will take several attempts to bend and check free movement of the shafts. Here is a picture of what I'm talking about (exaggerated in Photoshop to illustrate the tilt):
https://drive.google.com/open?id=0B9Ejm1yL02AGOTBGczF3QUtPaWM

Once everything was straight, the bed was much flatter and I could successfully print at .05 layer thickness. I think the Anycubic design team should consider widening the end mount footprint so that it would be less likely to tilt with small surface variations, or check for free rotation after they are mounted. I hope this helps anyone with print bed flatness issues!