Thanks for your information

see below
I removed the shaft above the Y motor (the shaft the Y motor turns and through that moves the axis).  However now that you mention it that stepper will be removed and a flat will be put in that output shaft as well before I am done.  I already (in another topic) ground a flat in my extruder stepper with excellent results (at least for me).

FairLoc(TM) hubs are designed to reduce the exact issue you pointed out earlier in this topic.  They are essentially a compression hub made out of aluminum but unlike the set screw they grab most of the shaft circumference.  SDP-SI sells them (this idea is patented) as alternatives for gears, pulleys and other applications where non-marring adjustment of that item will happen often.  There are other ways to do this, and FairLoc(TM) does require some regularity in the shaft dimensions, but in this case I can substitute these gear pulleys for the ones on the shaft without cutting a flat at all.  Effectively it is a drop in replacement.  As those 2 gear pulleys were obviously heavily tightened because without a flat they would otherwise slip.  My hope is with the FairLoc(TM) hubs I won't have that sort of issue.  Course as proprietary parts they cost a bunch more.

I bought 3 18 tooth FairLoc(TM) hub pulleys at basically $19 each.
I won't need one for the stepper because I will put a flat in that shaft, there is no rotational misalignment there that requires adjustment...just the need to stop it from slipping so the $5 existing stepper gear pulley is just fine.

You might have to break those free eventually. I know departed on here bought Fel-loc pullies I believe that have a different mechanism for holding torque that doesn't marr the shaft or strip. I should order those now in advance LOL

That is great. I ordered a new stepper driver 3 actually all over sized with heat sinks and I will print a small fan holder for the board as well. Once I hope I get it running. I will run prints without a fan,

As for the earlier comment about the rod alignment is so critical:
Once you dial in the alignment and tension the pulley location needs to remain fixed. because this is the main culprit of smooth carriage moment. So if you have the pullies set, that rod location needs to remain there (regardless of where the rod actually is a few mm left or right doesn't matter) but the location of the pullies on the rod does. If you shift that rod a few MM or knock the carriage could instantly bind.

I tried this dozens of times and it is repeatable.

Now with that said I found by having the rod flush with both sides minimize the risk of knock the rod side to since it is flush with the machine.

I tried to remove the front pulley-holders that are mounted to the frame but was unsuccessful with a hex-driver.
After destroying the grip for one screw I avoided to go for the back pulley's since I now suspect that they are not hex but in fact something else. Please do tell (the screws are really tiny and I can't tell)

As for the earlier comment about the rod alignment is so critical:
Once you dial in the alignment and tension the pulley location needs to remain fixed. because this is the main culprit of smooth carriage moment. So if you have the pullies set, that rod location needs to remain there (regardless of where the rod actually is a few mm left or right doesn't matter) but the location of the pullies on the rod does. If you shift that rod a few MM or knock the carriage could instantly bind.

I tried this dozens of times and it is repeatable.

Now with that said I found by having the rod flush with both sides minimize the risk of knock the rod side to since it is flush with the machine.

The culprit turned out to be completely non-mechanical.  As jjcuff1 had suggested, there turned out to be a problem with the y-stepper driver. 

I suspected something might be overheating, since the defects tended to start occurring in long prints, in higher layers.  So I pointed a large CPU fan at the electronics board with no cover on and ran some test prints.  The skipping vanished totally - not a single error in hundreds of layers now.  The picture attached shows a before (left) and after (right) comparison.

So how can you recognize this sort of error?

-Small skip size - no bigger than maybe 2mm, usually much smaller.
-Occurs later in prints (need to be intensive - not just single walled cylinders and such)
-When the glitch occurs, the machine will quietly, and very briefly stop moving the y-axis, just long enough to cause the small skip. 
-It does not sound loud, like a skipped step would.

This is almost certainly a result of the high demands on the y-stepper, as it is already pushed to the limit of its capabilities.  I am not sure why so few users have encountered something like this.

Thanks again for the help, to everyone who contributed.  And to Kvirre, I will use some of those tips as I optimize my backlash now!

My y-backlash problem has NEVER been trimmed down below 0.3 mm.

The most efficient way for me to test this without printing and measuring on the actual model, was to put my fingertip in the "gap" between the carriage-bushing and the rod and start this test :

• Step 10 steps a 0.1 mm in one direction

• Step X steps a 0.1 mm in the other direction

Repeat this for a different y-axis origin (back and front)

It's very easy to "feel" when the carriage starts moving in the other direction.
For me, the first reversed 0.1 step never translates to a move, but at best the second or third does.
(while doing this, it's also easy to observe how the different belts loosens and tensions)

Now you may try to loosen an tighten your belt.

To much tension renders in friction on the small ball bearings holding the rod & pulleys.

The Carriage :
I also tried loads different grease / lubes since the static friction is so much greater then the kinetic friction?
Guess that has to do with how sleeve bushings work compared to linear ball bearings.

Why did it turn out to be important?  My back rod isn't perfectly centered (off by 1mm), but I didn't think it would be an issue since I just let the loose pulleys align themselves before I tightened everything up.

So at this point I see only three main possibilities:

1.) The y stepper driver could be malfunctioning, like you said.
2.) Alignment/tension is so exceedingly sensitive that I couldn't get it right after 20-30 tries.
3.) The small wobble in the back rod is causing problems with the belt tension.

I am not sure what else could be wrong at this point.

So after alignment should eliminate skipped teeth. But again the skip steps in the servo I noticed like you over infill and extruder head popping and the stepper driver could have been under or over driven and caused it and probably just crapped out and over heated.

I also noticed that my belt problems started after the Extruder Ribbon was popping on the Y belt on the left hand side after long runs for a few days. I think that pushed the rod to the left causing my binding. And after realignment I realized how sensitive that back rod needs to be in right position to keep the pulleys aligned.

One thing I noticed is that the problem seemed to start shortly after I was trying to print an object that had alot of curling problems, causing the extruder to constantly bump into the curled parts of the object.  Before, this didn't seem to be an issue, since it never skipped.

Could these collisions be wearing down the belts for the y-axis, particularly the main belt?  I believe the tension was quite high, so it might be that the drive was pulling so hard that it skipped some teeth and eventually started to grind down the notches on the belt in these skipping events. 

Also, has anyone ever had issues with the pulleys getting dirty and needing to be cleaned out?  I am wondering if that could be it too.

I am gonna replace with stronger board that handles cooling and load better and order a new y stepper that can handle more torque and at 1.2 only from qu-bd.

with more torque at the right Amp limits of the electronics this sensitivity to binding issue should go away and allow for some mis alignment. My carriage I feel is totally smooth and dialed in. with my current belt tension. Unless the tension is way off, when it is smooth, no power, you should be fine.

Then the only adjustment you should have with belt tensions it to adjust to get the perfect circles little tight/loose to dial it in. BUT if these little adjustments are causing failed prints randomly and over sensitive it is more then belts it is probably the hardware.

I have seen at least 4-5 threads here started by different users all with same symptoms I can not imagine all 5 of us can not execute the same circle procedure to get machine right. It must be failing hardware

Kvirre, thanks for the advice on the main drive belt.  I have tried many things, but loosening the tension on the belt directly attached to the y-motor has had the most noticeable effect in mitigating my skipping problem.  I have had a couple prints now with 0 errors, which is major progress.

However, I still have some issues with my setup, even if it works for now.  The tension is clearly too loose, as the surface quality is quite poor.  When I had it just a bit tighter, the backlash was practically nothing, but it encountered skipping.  It seems that the system has become extremely sensitive to increased loading. 

I can tell because when the y-axis is moving, I can barely push on it and it will start skipping.  I recall it being much more resilient before.  So I have a few questions:

1.) Just how sensitive have people found the y drive belt tension to be?

2.) What could cause the "maximum load" of the y-axis to change?  Can the belts become worn with skipping events?  Can they get clogged with some material over time?

3.) My y-axis is currently at about .52 volts.  How high can I push it safely?  I want to extract significantly more torque.  I am thinking that it is OK to push that one harder since it is partly "heatsinked" from being affixed to the frame.

4.) There is maybe half a millimeter of bow in the y drive-rod (the one that links the two y-guides).  Is bowing a serious problem with this rod?  Should I get it replaced?

Thanks again for the help, everyone.