1) To flash the MK3 menu, it's best to use Neo Max (not Neo Power Kit).
Format the cart in NDS mode, add the menu rom and click "single rom". It should flash the menu to it.
2) At the moment, it's sort of hit and miss. Running from the SD card is ALWAYS slower and less compattible, but the size of the rom seems to have less of an effect on it, although bigger roms are less likely to work due to crashes because of the data not being transferred quickly enough.
3) It always takes a LONG time to flash a rom, and perhaps it's just me but it seems that the bigger the rom, the longer it takes to flash (As in if it took 5mins to flash a rom that was 256Mbit, then in theory it would take 10mins to flash a rom that's 512Mbit, but in the end it seems to take more like 15mins)
4) Currently, no, but when the menu software is updated, it will be able to hold more than one eventually.
5) The rom size probably wont change, except maybe get a little bigger (if any patching code is added) but always remember that Mbit and Mbyte (or Mb) are NOT the same thing. If a rom is 16Mb in size, it's a 128Mbit rom.