I'm now converting my first CD-ROM motor for e-flight, so I have faced some of the same questions you have posed.
My motor uses a 3mm shaft and ball bearings from a GWS IPS motor. Both components are readily available as spare parts from many vendors. GWS 4mm shafts and bearings are also available. So if either 3mm or 4mm components will work for you, these are inexpensive solutions. Another source for bearings of many sizes (as well as countless other parts) is McMaster-Carr
To secure the shaft, I designed the motor to use the stock e-clip. At the other end, a small washer between the bell (rotor) and the stator prevents the stator from contacting the bell.
Here are a couple of photos. I still have to replace the stock ring magnet with N45 magnets. The finished motor will weigh more than an ounce, much heavier than some. For my next attempt, I will use lighter weight materials instead of all that brass.
Here is a test assembly of the motor. A couple of washers will go on the end of the shaft, then an e-clip to hold it in place.
Here are the major components, except for the stator. I soldered a length of 9/32" OD brass tube to the original stator hub. The 1/4" OD aluminum tube slides into the brass tube and is swaged to accept the 6mm diameter ball bearing. This would have been a much easier project with metric-dimensioned tubing, but I have not been able to find it in small quantities.
Below is a photo of the ball bearings. One is CAed into the original stator hub, which has an inside diameter of 6mm, the exact diameter of the GWS ball bearing. I enlarged the end of the aluminum tube with a screwdriver to accept the other bearing.
If metric-dimensioned tubing had been available, I would not have needed the aluminum tube. The only reason for the aluminum insert is that I could not figure out a way to swage brass tubing to accept the 6mm bearing. My metalworking tools (and skills) are modest!