With the ability to tram the Z-car being very limited across the Y axis this could be a good time to address it. I've just completed that process with my BT-48a, the only difference being I used a verified thickness straight edge across my powerstick whereas you would use it across your extrusions. I mention this because I found that the cause of my out-of-tram was the gantry being nearly 2/10" higher on one side than the other, thus throwing the spindle off perpendicular.
I was able to resolve this by placing a thick shim on the low side between the blue vertical gantry plate and the main extrusion it's mounted onto. I was concerned that there would not be enough wiggle room to raise it that much because of the mounting bolts that attach the gantry to the outside of the big extrusion so I was prepared to use smaller diameter bolts there if need be, but it wasn't necessary. In fact, I really lucked out. My first step was to scribe the gantry location on the extrusion, loosen the top and side bolts and slip a steel ruler between the gantry and the extrusion to see what happened. As luck would have it, the variation between the two ends of the gantry was now within 2/1000 with the bolts re-tightened. I was able to squeeze another 1/1000 out by resetting the bolts holding the spindle to the Z car while applying light holding torque to the side of the spindle so I now have slightly over 1/1000 misalignment on the Y axis using feeler gauges under a 10" diameter tram. Things do not always get that lucky!
Next I went after the Z axis which was less of an issue at about 7/1000 misalignment. I initialy went with shims between the back of the spindle and the mounting plate but my gut told me that was not ideal so I then went to placing "U" shaped shims over the mounting bolts in behind the V-rollers. In my case that was the lower ones but it could be either depending on whether the alignment is fore or aft. I quickly found out that using plastic shims was not a good idea because they extruded out quite a bit when the V-groove bolts were torqued down. Once I switched to metal shims this was no longer a problem. It took a little longer this time but I am now out on the X axis by 1/1000 across the 10" diameter tram circle using feeler gauges. That's 1 thou and 1.5 thou, far better than anyone machining wood really needs but it was a fun exercise and should reduce the potential for snapping off small diameter cutting tools.
It may not even be an issue with your machine of course but hope that gives you some food for thought as it appears you're rebuilding your machine to tight specs.
Shopbot Buddy BT48-12z alpha
2', 4', 8' Powersticks
Shopbot indexer
Shopbot airdrill
4hp HSD spindle
Aspire 4.5
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