Y axis stalling

[JAZZCNC]

OK, before I take things apart a bit more and get lost, here is what I have found.

1. The motor knob becomes stiff when the leadnut under the gantry can be at almost any point along the length of the leadscrew, i.e. not just at the ends.

Ok you can't feel for stiffening properly with the motor connected because of the Detent of the motors to do it properly you MUST remove motor.

I'm thinking that there could be two ways for bending the leadscrew. One if the leadnut was not mounted centrally, and the other if the chassis is out of square or the leadscrew not exactly in the middle of each end piece. How can I check for all of these? Because there is also the possibility that a bent leadscrew has been fitted at the factory - which I'm hoping is the case and my machine is fundamentally sound. Also I would not be that bothered if the leadnut was not mounted centrally because if I convert to ballscrews I would be fitting a new mount.

Without seeing the exactly how the ends are fixed and the leadnut mounts to gantry then it's hard to say. But if it's how I think then to get a rough idea you'll need to remove the bearing at one end and the run the gantry to that end with leadnut attached and see if the screw is central in the hole.? This should give you some indication if it's misaligned.
The most common reason for bending is because the leadnut is either lower or higher than the ends in middle of it's travel where it's the most bendy it then lifts or pulls down on screw when approaching ends bending screw in process.

To check if screw ends are equal is a simple case of measuring from one reference edge to screw centre(or edge) for both vertical and horizontal. IE: Machine side to screw for horizontal and End plate edge to screw for vertical.

Then if ok loosen the leadnut mount from the gantry so there's no pressure on it and run the gantry to one end. Now check for any gap between Mount and gantry.? Now Run the gantry to other end and see if the gap is the same. Do the same at several points along the screw.
If all is ok the gap should be same or very very close to none, ideally you want light interference fit.! Now it's just a case of shimming the gap so when tightened there's no pressure or pulling on the screw.
If there's no gap and there's tight fit between leadnut mount and gantry then you'll need to remove some material from leadnut mount.
If your leadnut mount doesn't bolt onto flat surface and instead has drop bracket that which fastens to gantry cross brace then you'll need to loosen the bracket to slip fit and put witness marks on bracket and brace. Then run gantry up and down it's length and watch if marks move.? If they do then try loosening lead nut from the bracket and find balance using both bracket and leadnut mounts, failing that you'll have adjust the end fixings.!!

If the machine is out of square then you'll feel it going tight when pushing gantry up and down it's length with leadnut disconnected. Being honest thou with the sloppy linear bearings on these machines I doubt you'll feel it. That said for it to be bad enough to bend leadscrew you'd most certainly be able to visually see it.!!

Obviously I'm giving adjustment suggestions blind has I can't see your machine and how things are fixed but hopefully should give you an idea of what i mean.!!! . . .. . . OR I could have just blown your mind. .