dmitryk

1st question. USB 2.0 with a rate of 300MB per 15 sec... will produce 20MB/s
That is ok for USB 2.0 if it has only one device on that bus... In genral it's close to it's limits... and I would suggest to consider either Firewire 800 or eSATA - external SATA drive.

2. You shold not lose data when you convert from FAT to NTFS, but....
if filesystem is corrupted in a first place, or you lose power , or hdd has abad sector or.... Backup before you do anything which compromise data integrity ;-) and verify that you backup correctly.