Don't use a pitch shifter on the entire song. There's no need, and it makes its job a lot more difficult.
Apply pitch shifting only to the parts you need to. Drums and piano won't need it. I assume drums will sound fine with no pitch shifting, and think of how much less work the pitch shifter will have to do without all that sound washing over everything.
Piano can be shifted easily in the MIDI itself by transposing the notes in the MIDI editor. That will sound most natural.
That leaves bass, guitar and vocal. If the bass was MIDI, just transpose the MIDI notes like you'll do for piano.
So for the parts you recorded acoustically: it's best to use pitch shifting on mono sources, one at a time. Gate any background noise that's obvious first. Give the pitch shifter a fighting chance to do its job. Then pick the algorithm and settings that make sense for the particular part. Your settings of ReaPitch will vary from track to track because the sources will sound better with different algorithms and settings.
The best thing would be to re-record any parts you can at the pitch you prefer. Failing that though, treat each mono track individually with an instance of ReaPitch, and the MIDI can be shifted in the MIDI editor (and drums don't need shifting at all).
Perhaps you want the pitch of the MIDI parts shifted to something slightly off from a perfect division of pitch. I'd say do this first: shift the MIDI as close as possible by solely transposing the notes. Match your pitch shifting on the acoustically-recorded tracks to that MIDI. Then you can apply a slight pitch shifting to the MIDI and audio: pitch shift the acoustically-recorded parts that little bit more, and add a pitch shifter to the MIDI parts' audio output to shift it that little bit more. And don't shift the drums since that's not necessary.
Avoid having any pitch shifter on a track or bus with reverb or modulation/delay effects. That comes last. Pitch shifting should be done on tracks that are bone dry, with as little noise as possible. The pitch shifting can then do its best for the particular source, and you won't have to be concerned with how it affects anything in the background of the track which might not take the pitch shifting well (with those particular settings for the intended source).