Y-axis "hangs" randomly

its known as 'skipping' and is caused by a multitude of possible reasons - however - the most common is the thermal protection on the Stepper Driver IC's kicking in which causes a momentary shutdown, however, since the printer has no idea this is occuring, it continues on its merry way with the affected axis now out of position.

So one Solution: Put a fan on your electronics if you dont have one. You can confirm the issue by putting just a standard oscillating fan blowing on the board, and if it does indeed resolve the issue - print one of the many covers that include a fan.

(if you search for skips/skipping/missed steps -  you will find tons of references to the problem/issue/solutions)

I have this problem too, but it is just a warped bed. If I do a fast move on the first layer, it might catch on filament that has already cooled or just make a line in printed material that is still hot. This is with glass on the warped bed too. So, at some point I will need to adjust the warp out of the bed. Meanwhile, if your printed object is small enough, put it to the right or left of the centerline and see if it still "skips".

It seems as though this has been a problem for several users lately.  First (I can't emphasize this enough!) Calibration and alignment of your belts is vital.  Everything should move smoothly by hand when the drive belt to the motor is removed.  Then as a quick and dirty test reinstall the drive belt but don't tighten it too much maybe even slightly loose.  This will induce backlash but that can be adjusted out later.  The other thing that most people are intimidated by is adjusting the VREF's  It isn't that hard and there are numerous posts about the process.

I am happy to help you through this.  The looser belt will reduce friction and tell us what the problem is.  it is just a test.

Ok so with that belt removed how does the Y-axis move?  Nice and smooth?
I like to loosen the set screw for the right drive pulley for the Y-movement.  Then slide the carriage by hand  back and forth until it feels like the right side is resting in a nice neutral position then tighten the set screw.  This will align the two sides and eliminate another source of binding.
Next is more of a question you should already have the answer to.  Is it over extruding?  Meaning when you print, is the nozzle constantly dragging on the previous layer even just areas of the previous layer?  If it is then let's address that before you move to the next step.
Time to adjust your VREF's.  Something is causing that axis to skip.  This can be caused by several things and the loose belt eliminated the Y-rod binding so snug that up (not to tight for now).
Each stepper driver has a small potentiometer on it that adjusts the voltage going to the motor.  This is easy to adjust and can be done several ways.  It is important to note that very small adjustments go a long way.  So find a small flat screwdriver that fits.  ideally it should be plastic or ceramic but a small glasses screwdriver will work.  Just make sure you don't short anything else on the board.  Locate the Potentiometer for that axis and (guessing here) turn it up in increments as small as you can move it.  Run that axis and you will notice the sound change.  If you tune it up or down to much the motor will stop moving so you are looking for that spot where it sounds smooth.  At this point you should be able to hold some resistance against the axis and tell where it seems to have the most torque.  I do this by pinching the Y-rod between my thumb and finger.  Just to add some resistance.  If you get to the point that it moves freely this way then it should be good to go.  If it then skips during printing you have other issues.

Unless you are saying you actually shorted something out and don't want to admit it.  I highly doubt something is wrong with your board.  restart everything and check your com port.

So many things that could cause this.  I would start with the basics since you replaced the board.  Re-check every connection then double check them.  Make sure the power supply is functioning as well.  The board will connect through USB alone but how are you able to tell that it isn't connecting.  Please remember I don't use a printer board and never have.  My Rumba needs the power on in order to connect to the PC.  I don't think that's the case for the Printer board but it's worth checking.
Also I know most of the connection problems I have seen are rarely caused by the board being bad.  I have read many times that "Reset on connect" needs to be disabled (I Think) so check that and also that you have the correct baud rate set.

My bad got confused with another user.  Brain gets scrambled sometimes.
Doesn't change the process of troubleshooting your problem though.
Have you had any conversations with SD Support?