OK, to be honest I am a bit confused now.
Obviously I have missed something.
Sorry about that.
Setting the motor current is a completely independent thing from adjusting the number of steps per mm.
Setting the motor currents will only adjust the amount of power the motors receive from the control board, and in turn that will adjust the amount of torque the motors will generate.
Because these are stepping motors, the steps/mm does not change if the drive current to the motors are changed.
It is always 200 full steps per revolution on the standard Folger Tech motors regardless of the motor current and this will not change unless you change to different motors.
They are then micro-stepped electronically to achieve a finer resolution and smoother operation.
For example if you are 1/16 micro-stepping them, they will require 3200 "steps" to complete one motor shaft revolution.
Past that, the number of teeth on the motor pulley, the pitch of the belt and the number of teeth on a driven gear like the Z axis determines the final "steps/mm" setting.
None of this changes unless you change out mechanical things.
But if the current is set too low (sounds like it is OK though) the motors cannot provide enough torque and will go "out of sync" to the commanded motion steps.
In other words, they will stall and skip steps.
If your new track and carriage are binding, there is something wrong with them and they should not be used.
They have been damaged somehow, perhaps in shipping.
I assume that your printer is using the standard FT setup with two Y motors, right?
Loosen up the screws that fasten the X rail support plates to the Y rail carriage on one or both sides by at least one full turn.
I suggest doing at the left side for sure because it is much easier to get to.
Home the motion first and check to see if the X bar is parallel to the framing.
Then using manual motion commands in the user interface or Pronterface or whatever, run the Y motion at normal print speeds (if possible) from back to front and back again a few times in a row.
Don't re-home Y between the motions.
If it does not bind, skip or rack (go out of parallel with the front or rear cross bars), tighten the carriage screws again and repeat.
If it then binds, the problem is very likely that your tracks are out of parallel horizontally or are skewed vertically from side to side.
But if it does bind, skip or rack even when the screws are loose, you will need to either slow the motion down, increase the motor currents, or the tracks may be extremely out of parallel in one axis or another (don't forget vertical).
Measuring with a tape measure is not remotely good enough to see if they are parallel by the way.
And the two sides could also be out of level with one another.
I have long disagreed with the method for installing them in the manual by spacing from the top-most rails (sorry Chris).
The mechanically safer method is to use a 19 inch long piece of dowel rod or conduit as a spacer and to adjust all four corners of the middle rails from the base of the printer.
The precise length of the spacer is unimportant as long as you use the very same piece to adjust all four corners.
This is because the base is by far the more stable and reliable of the two reference planes.
It is also, IMHO, much easier and quicker to do.
Sorry for the novella, I am just throwing out everything I can think of to try to help.
Clearly something is out of whack.