CPAN has enough to accomplish your task.

The adding a second of silence part can easily be done with Audio::Wav::Read and maybe Audio::Wav::Write. One second's worth of silence would be represented as sampling rate x channels 0 samples at the beginning of the wav.

As for encoding an MP3, you could use Audio::MPEG which interfaces with LAME's library to encode MP3s.

update: minor repharsing in second paragraph.