Hi Marc,
The sheet music you get from a .mid file may not necessarily match exactly sheet music that you have bought. Notation Musician will give you the transcription of the MIDI file from the data that it has, which is dependent on the person who originally sequenced the file. Sometimes it is the same, sometimes it is different.
To use the MIDI file that you have, you will need to (1) merge the Lyric and Clean electric guitar staves (Staff/Merge) and then (2) use the Part/Prepare Fakesheet wizard. When you do the Chord transcription, you'll probably only want to use the Acoustic Guitar and Bass staves, and use the "Easy chords" option for the chord transcription (Options).
It will still be somewhat different than the pdf file you have, but it will look much more like it than if you use all staves for the analysis.
Enjoy
Sherry