well a good base rules that out as a possible problem.
I use a man made Flat smooth stone floor tile on top of a 1" thick foam base sitting on a strong table. i've made sure everything is as level as possible then placed the machine on that. a lot of people use folding tables and what happens is they sink in different spots over time. so my idea was isolate the machine from the table on a solid base.
on a solid level base you will also see if any of your legs have lifted indicating a twist in the frame.
with all that out of the way:
look the machine over for obvious hardware that has gotten loose from vibration. turn the machine on its side and inspect everything under the machine, double check the nuts on your frame and make sure nothing got loose. check all the motors that the hardware didn't back out or something.
if everything looks good, then start moving all the axis by hand and see if you feel something sticking out out of place. i oil up my rods using Slot car motor oil for lubrication just light and i work the oil in by hand around the rods so a light coating. the bearings kind of work themselves in and the tolerance opens up. i've had to go back later and loosen the U bolts on the bearings and kind of reseat them then lightly tighten the U bolts back up to avoid tweaking the bearings.
next if you find nothing or have made corrections you hit the belts and tighten them up as they loosen up from new then kind of hit there stretch and normalize. make a mark on the Belts next to the Extruder belt holder on the X/E axis and on the belt holder under the bed. you will only ever move one side of the belt. the mark is so you can see your starting point, and i make it next to the holder then i stretch the belt one tooth so i can visibly see my mark move one tooth on the belt or you may need to go more then 1 tooth. the belts have to be pretty tight and you will be using a little muscle or some pliers to help you stretch that belt.
after all that. re run XYZ cal and see where you are.
now during all the messing around with the frame and belts i found a great method for truing up the alignment of the bed and X axis. i place a straight edge on the frame in-between the Z axls motors and move the bed so that the straight edge shows alignment with the grid on the Bed under the PEI sheet. you will obviously see all the misalignment you then have the tweak the Y axis frame rails through the frame to skew the frame so that the Bed sits straight between the frame rails. now this method skews the frame a little but the Y axis will be parallel and the X axis will be lined up with the bed.
All the PETG 3d printed parts on the printer have different shrink and are not perfect so if you build everything square it will just always be off. so i found you have to shew things a little.
the printer will squeak and make some funny noises for a little while until the bearings and rods get used to the new configuration but i have skews on my machines of .01 and .02 compared to my MK3 which is .08. keep everything oiled and inspected and after a day of printing the machine will stop making noises and start to free up. the machine had to like break itself in. then every week or so re-inspect the machine for problems clean it up re-oil as needed and run the XYZ cal and see if things are holding or still moving around.
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