Many machines have two Y-Axis motors. If something goes wrong and you hear the grinding noises, the Y-Axis carriage will not be square with the X-Axis carriage. To fix the problem, you have to move the Y-Axis carriage to the back of the machine and square the Y-Axis carriage. This assumes that you don't have limit switches at the back of the machine. Is it possible to put timing belt and pulleys on the Y-Axis motors?
Need some more info. What machine are you talking about? LinuxCNC can offset the independent y motors. You do need limit switches.
I built my own CNC router using parts from OpenBuilds store. I have homing/limit switches. I have CNC XPro board and GBRL Panel software.
You don't have to ram the machine into the ends. Just place a spacer between the end plate and the gantry plate. I use two identical pieces of 3mm thick carbon cut off. Once you get close, just turn the feed down so it isn't violent. The spacers keep you from hitting the limits. Then home the machine again. This only works if your machine is actually square though. Adding a belt/pulley configuration to connect both sides will kill the entire purpose of using lead screws. (A very short belt gear reduction would be an exception.) The other option is to just use a single center mounted stepper. For something like that, I wouldn't use wheels.
the Z extensions are not helping with your stiffness, is that mdf peg board? Use shielded wire for your steppers and limit switches. I've never had the two y's on my machine get out of sync, but... bigger motors and not an x-Pro too
If it was me working this then I would do the following. I would square it up. Measure diagonally from corner to corner. The measurements should be the same. I did not have the best luck with the x pro or grbl. I would use better stepper drivers and linuxCNC. I know some people like the grbl but linuxCNC works a whole lot better. It is the same price. I would stiffen up the X carriage some how. Looks like you are off to a great start. You should be able to make some cool stuff with it.
I squared the machine as best as I can using a square shown at Empire Magnum Fat Boy 7 in. Aluminum Rafter Square-2990 - The Home Depot After homing the machine, I measured the distance between the gantry plates and the end of the C-Beams. After making the distances the same on both sides, I used a Sharpie marker to mark the lines on the C-Beams. I will have to buy a new trim router for my machine because the DC can motor may have bad bearings. I usually don't have problems with the CNC XPro board or GRBL code. I replaced the hardboard brackets with 3D-printed brackets.
I burnt out a driver on the xpro. The grbl programs seem kind of buggy to me. I was constantly shutting them down and restarting. Good looking machine you have there. let's see it move.
I bought the Makita RT0701C router yesterday and started 3D-printing router mount for it. I put the router and mount on my machine and cut out a part for a model car from plywood. The new router cut the plywood better than the old DC motor.
