My Mum's Kobo touch hasn't had these problems so unfortunately I can't help you there but as for the micro SD card question.
I installed a SanDisk 8GB microSDHC Memory Card (Class 2 speed performance rating) in her reader and side loaded quite a few books (between 50 and 60 in total I think) over that way for her and she's experienced no problem with accessing/reading these titles.
Kobo boots quickly, so does the library/books when accessing them and all the questions you mentioned I asked her and she's had none of these problems herself. I would immediately know to be honest, any problems with techno devices, be they readers or her laptop I get handed over pretty quick to attempt to fix.
Hopefully someone more techno-savvy or whose has experienced/or heard of these problems will be able to help you fix these.