At least you are cutting parts but much to much drama to get there.
Three spindles were installed but no finish issues. To replace a spindle from Haas spindle is to fail vibro. Only once have I seen vibro meet specs. and have poor finish issue. But your issue was positioning. Ballbar program is small and produced sucessful circularity during ballbar test. Maybe the FIR parameter values were not all the same. With a large program the processor might lag on processing positoning of an axis. For a while this was seen when adding a 4th or 5th axis.
Sounds like they just altered a parameter and problem solved. Less the aggravation your machine might be just fine. Service from local HFO, different issue. best of luck.