I have a very similar problem with a very loud clicking and hesitation as the y axis tries to move

I had a similar problem which turned out to be bent Y rods.  If you moved the carriage front-to-back with the power off, you could feel it grabbing at various places.   Rather than replacing the guide rods, I rotated them until the carriage moved without binding. If you loosen the hose clamps that are on both ends, and rotate one clamp all the way clockwise, and the other all the way counterclockwise, and tighten them, the rod will be trapped and can no longer rotate.  Then the carriage will bind less. 

I'm not saying that this is your problem, but it could be contributing to the problem.

I will rip her apart any way, seems easy, just to be sure. I tightened the belts and the collars to the pint that the belts were too tight then backed off. Still had issue.

I did consider the filament pulling issue. I use the stock location with it horizontal. It has pulled no problem for week now and when testing these last few days I did purposely pull up extra slack to make sure there was no load on the head. It didn't seem to make a difference. But why would it occur now when the spool is half full vs new so should be lighter and pulls easier and it doesn't happen in the first few layers always at layer 5-6 and then continually steps back wards

I will check the voltage
check the belts (maybe a tooth is worn)
and for testing I will cut a predefined length of ABS to the length needed for the print to ensure there is no drag

It does seem to have more noises then last week, and I do leave it plugged into the USB over night (not the power) so the PCB always is powered red not sure if over heating things?

It definitely seems mechanical though since the first few layers are always perfect, level bed etc heat flow thickness all look great, even the bad layers you can see are laying down right just shifted back. So I assume the slicing is good.

am wondering do I turn off the z wobble code? I can not imagine the z-wobble would cause a 1/4" shift in just 1 direction.

The good news out of this. I really have identified where my level bed should be located, how to control my layer squish (zstop) and how to reduce the squish and still get sticking by playing with flowrate slighting with the RH slider. My first layers really look good and are consistent.

I just want to start making my parts DAM lol

I will do one more LARGE print as a test to see if this is really effecting the small prints near the middle of the bed but the largeer prints now. (which would mean acceleration and speed on small jobs is causing overshoot.)

The pulleys on the front spin freely over the bolts rather than being fixed to a rod which itself spins, so they don't need set screws.

Well no luck just did a cube and still no luck z is shot I think my shit is broken useless machine now and so random works perfect then next one nothing

1: Check set screws, and tensions (but I think they look ok)
2: End stop check, simple. I definitely have noticed a lot of cable dragging in that corner and I am concerned it will get ripped. Have to print a guide.
3:Bed Level. I am wondering if my bed level is too close to the extruder and is pushing the front of the bed down. Then once it clears enough height the bed springs release the pressure but now the print is tilted because the front pops up and the back drops down. Look at 3rd picture it looks squished just up front?

I had a gear print that would suddenly run a perimeter straight across and offset the whole thing at the same point every time.  It turned out that I was getting false endstop hits for no apparent reason, maybe because a wire was going bad or something.   Keep an eye on the log window and see if it starts saying Enstops Hit when the skipping begins.

Well day before I printed some large rounds came out great. I leveled the bed shut the SD2 off and last night I went to print a small 3" round part and it started great up to layer 5. Looked normal. walked away and the print totally shifted to back of machine able 1/4" or more and it kept printing and walking back and back! I killed it at 16

well I releveled re did cal cube all was in spec but still tweaked a little slowed speed down by 80% even and it was repeatable at the 5-6 layer i literally could hear the extruder and see it bum over and start the layer 1/4 in the y back.

So I slowed it more enabled M99 even (I already had z wobble dialed in) I netfabbed my model then printed known working models and they all kicked in at layer 5?

Then I slowed down even more, re cal again and with M99 at .17 it improved slightly but it was around layer 9-13 then it would kick back it looks like to the front either way the models were junked

WTF is my bed that out of level and it is just pushing the bed down? Thel1st layers look and stick well which tells me the bed is fine. is the Y WOBBLE SKIP THAT BAD? i can not believe it it looks like software thing? HELP

Look at this first 5 layers great and perfect then wham kicks over 1/4"

and here is my last print just prior to running this with NO CHANGES:

Only thing I can think of is the y belt skipping but y after the 5th layer? I tensioned the y and the brackets do not look broken or cracked but have to look again

I did z wobble but has it skipped? I did extensive z wobble dial in and happy with results no banding. and now it changes this drastic?

Is the stepper motor bad?

or maybe was there last few days but my prints were not in the middle of the bed, they were large and on outside of bed. I would think that would be more difficult to maintain then the middle.

or slow it down further to 20mm/s