I tried Bitcoin Armory to import multiple priv. keys (few thousands). It was fast. It took about 15 mins for all the process. and the rescan was very quick.
Well, I'm trying the same with 900 private keys, but it takes more than 1,5 hour total already.
importprivkey "5yourveryveryveryverylongprivatekeystring" "my-new-key1" false
importprivkey "5yourveryveryveryverylongprivatekeystring" "my-new-key2" false
importprivkey "5yourveryveryveryverylongprivatekeystring" "my-new-key3" true
The last true triggers the rescan, other false are skip that. So you scan once for balance at the end.