Many parts are cast, so thats why the holes are off centre.

These Chinese things need urgent controller change for sth better. As that is the very nest of problems on any machine, the unstable controller.

Spindles and VFd normally are Not a problem. Most VFDs have a Voltage input adjustment so it make regulating RPM very easy. All must be properly grounded also or you will never get stable RPMs

Obviously all should be properly aligned and centered as i wouldn't trust a cheap machine has that right. meanwhile Locktite on all possible parts so to avoid future problems.

Start with posting model of VFD here, i or others may help.