Just load the file into a PGPPublicKeyRingCollection and then iterate though each contained keyring until you find the key with the matching fingerprint! One of the BC PGP examples has 90% of the code you require for doing this!
As far as "Is .gpg in GNUPG equivalent for both .pkr and .skr files" is concerned then I'm not sure what you mean by 'equivalent' . As far as I remember the pubring.gpg file has the same format as a '.pkr' file and the secring.gpg file has the same format as a '.skr' file but you can't use the same
Java BC code to load both. If you look at the BC examples and Javadoc you will be able to extrapolate from loading the public key file to loading the private key file.
Since this project sounds like it has a large number of PGP key I'm surprise you are not using a database to hold the public keys. I use a MySQL database for public keys with an index on the email address, the fingerprint and the customer name.