Hi Chris, its actually a good idea to use flanged bearings in this situation. As you deduce, it avoids the outer ring from sitting cocked in its housing. It also means you can slightly loosen you bore tolerance. But the inner rings / shaft are still a little vulnerable from two things. Firstly ensure that your shaft shoulders are square to the shaft by machining them in the same operation as the seating diameter. (Watch that deadly corner rad. too!) Secondly the shaft must be accurately square with the outer rings. Therefore machine the two housing together and make sure they stay in the same relative position after the frame is assembled. If you want smoothness and minimum friction, alignment accuracy needs to be in the order of 0.05 degrees.
Regarding your damaged bearings issue, one problem is that the manufacturers typically use in the order of 50 to 100 different greases to meet specific high-volume customer demand. Local stockists don’t usually care about what’s in the bearings they sell to you unless they are asked to supply a particular grease type. So basically there could be anything in your bearings from a simple mineral/lithium thickener type, to silicon, PFPE, diester and all manner of other stuff. Usually the grease type is marked somewhere on the packaging if the bearings are individually boxed. If yours have come from a multipack, there will not be traceability now. I would suspect that you may have suffered from an incompatibility issue.
Please keep in mind though that grease is a combination of oil and a thickener. Thickeners are not soluble, only the oil component is, so dipping them in a ‘solvent’ is not effective. You really need to at least remove the shields.
Alcohol is not great general purpose grease cleaner. It can contain water and/or absorb it from the atmosphere so I would be wary of using this this for bearings. My preference would be brake cleaner from an aerosol can, as it will be filtered to fine limits. The jet will also help blast the grease away, mechanically.
Finally, if you take shields out of small bearings they will be damaged and you cant put them back in. So try to get hold of bearings with what are known as ‘non-contact seals’. These are really shields but made in rubber like normal seals. They have a much finer labyrinth than shields though. However, the real beauty of non-contact seals is that, with care, you can pop them back in after cleaning the bearing. When re-fitting, make sure they are absolutely flat, then snap them in using a flat plate. Non contact seals have the designation in NSK language of V, as opposed to D for a contact seal. Other manufacturers may have other designations.
Gerry