Aluminium Profile Type Router - Initial questions

[JAZZCNC]

The rubber part is only on the dual Y (formally known as X :) axis) ballnut. As per below in red. The bolts are still coupled into the ballnut mount, but I can easily replace that with 1mm aluminium shim.

Dump the rubber it's a bad idea for the reasons stated before. Shimming with aluminium is the better way to do it.
What you have done so far with rails etc and screws is fine so with shims you'll get it pretty much spot on with a bit of patience. My point in all the other post's was to high light the difference and why the extra plate makes things easier and with less chance of messing things up in other areas when making adjustments to gantry.

I've attached the motor mounts now so am going to run it tomorrow and see how it moves. Is it obvious it its binding , does it judder etc?
Then if shimming is needed use this on the gantry and Ball screw mounts.

Be Very careful when approaching the ends of travel because it's here where most get it wrong and it's very easy to bend the screws. At slow speeds the steppers will quite happily bend those screws like it's liquorish sticks and not complain about it.
At higher feeds any error here will stall the motors but still damage will be done.

When jogging near the ends watch the ball screw carefully and if you see it lift or bend then you have some misalignment. I CANNOT stress this enough move slowly and watch carefully because it only takes a second to bend the screw.!!

If you see any movement then loosen the end bearings and jog slowly towards the bearing, this will give you some idea of what's wrong. Most likely either a Gap will appear between bearing and frame or it will lift up/down. However it could be pushing the bearing into the frame which isn't so easy to see so pay careful attention to what the screw does.

How should you align the ballscrews vertically - I tried using a DTI on the rail touching the ballscrew but hard to where on the thread it sat. Or use a small block sat on the screw..?
Do people use the 3, 4, 5 triangle method to check square then adjust and set limits? As there are various ideas out there..

Will report back after running it - wish my luck

It's difficult on a long machine to use the DTI because the screw sags so you need a combination of straight edge and DTI. However it's often easier to go by feel and just loosen the end bearings, then shim or adjust as needed.
Between adjusting the Ball-nut mount and end bearings you will get it spot on eventually but don't be surprised if takes several setups, but the effort will be worth it because any binding robs power and cause excess wear so the extra time spent here pays off BIG time.

Regards testing for squareness then if you haven't got precision squares etc just initially use a good set square off the master rail to get you close. Then just cut a Large square, nearly the size of your bed and measure the diagonals with a good steel rule, NOT a tape measure. Tweak and adjust as needed then cut another square by trimming the last one.