How to make a device in miniSD or microSD form factor?
I am not very sure what are your manufacturing powers, but here are some considerations:


You can use flexible PCBs. Produced on polyimide base they can be 0.20mm thick for two layers board and 0.13mm for one layer board.
You can implement the connection contacts as traces on this PCB. As long as the PCB is flexible you can use one side PCB and to bend it this way in order to provide some space for the parts:

connector 
_________     parts
         \__A__A__A__A______

Some very small parts have to be used, but considering your other questions on electronics.stackexchange.com you already have most of them.
BTW, if it is too expensive, or too hard to put everything in a SD card package, there is another solution, accessible even for an amateurs - put everything in small box that ends with SD card-like connector. This way, the thin part of the design will be only the connector - a piece of PCB with contact tracks:

                  ___________
 connector pcb   / BIG PARTS \
        ===================== |                
                 \___________/