A complete discussion of all the why's and wherefore's of bearing preload is far too complex for a venue such as this. For this reason, I can only refer you to a general explanation as found below:
http://www.bardenbearings.co.uk/index.cfm?articleid=717
The three most common methods of preloading are described in the illustrative PDF's. They can be downloaded via fig 1, 2 & 3 from the Barden website.
I suspect your machine uses preloaded bearings in some positions (IE: ball screw support bearings) but they may use position preloaded bearings in the spindle if it is so equipped - they might also use spring preloads, especially if the spindle is a high speed one or one that has a lot of thermal growth potential.
THe "offset" that I"m referring to is literally ground into the face of the bearing ring - usually by the bearing MFR. at the time of production.
Essentially, the brg mfr takes into consideration the external loads and the thrust capacity of the bearing and computes a reasonable preload for the bearing. When the bearing is assembled, the "offset" is taken up and the design preload is applied as the rings are AXIALLY clamped together at assembly.
The preloading is TOTALLY different and a separate entity than the eccentricity high point markings.
This "preload reasonableness " takes into consideration internal friction/loading, durability and the external loads and the stiffness that is needed for the bearing to support the applied loads without deforming - this deformation is what can cause unplanned for tool deflection or chatter. Ball screws are especially critical in their need for preload as they are typically long (thus can stretch) and position accuracy necessitates that the support bearings be VERY rigid - thus they are typically highly preloaded.
Sometimes, there are bearing rework facilities that can do this type of preload work and or rework but they are few and far between. The only one I have worked with is KAF Mfg. in Stamford CT in the USA.
If the bearings are assembled and lubed properly, they will give hours and hours of essentialy trouble free service. If the bearings are not installed properly & the loadings are misapplied, the bearings can be damaged irrepairably merely by tightening them into place.
Although bearing suppliers will provide info on the generalities of preloading, they do NOT provide it as "do it yourself" information - the subject is simply beyond the realm of DIY as you have to take a lot of factors into considertation that most people a not equipped to do - especially swing wrench monkies who fubar machine tool "repairs" as you can attest to.
I catch a lot of flack sometimes about my 'high end' attitude toward bearing applications work. However, it is situations like this is what I try to prevent. Namely, to prevent some IDIOT who shouldn't be allowed near a machine to FUBAR it by doing things in a half-fast totally wrong "this ain't rocket science" fashion. What a waste of human DNA.
Sadly, you are the victim of miscreant DNA. WIth luck, perseverence and research, you may be able to minimize your losses.
HOWEVER, let there be no mistake about this, unless you can fix the damage and return a reasonable level of accuracy to the bearing fits and preloads, the machine will never run to even a fraction of its original design intent and potential. Sadly, in some cases, the only fix you may have open is to buy new bearings and, if they are ball screw support bearings, these tend to be VERY, VERY, VERY expensive.