Changing Intonation/Temeprament

You can change the tuning of each note in your score. Starting in version 2.1 it is easier. First you can go to the Synthesizer and change the tuning of A4 if you like (this is possible in al version 2.x). After that you will need to change the tuning for each note such as C4 and E3 and so forth. To begin, I personally would start by making a chromatic scale in the score that covers the range of all instruments and adjust each note in the chromatic scale. When I was done I would delete the measures with the chromatic scale.

Here's what you need to do, Right click on a note and chose select>more... In the more... dialog only select "Same pitch" it will even tell you which pitch you have selected. This will select every note in the score with the same pitch. In the inspector you can adjust the tuning of the note by however many cents you like and it will at this point change every note selected. You will of course need to do this with each note, since each one's offset is is varied compared to equal temperament. Since I don't know exactly what taking the trash out of your music will entail I'm not sure of any of the offsets. If every B-flat has the same number of cents offset, there is an option to select every note with the same name such as Bb. This will make it go a little faster.

This is actually not true, Polyphone lets you tune each sample (Select a sample, then under "Information" change the pitch in the input field labeled "Correction (cents)".
I found it much easier to send midi to an external player - fluidsynth i.e. supports on-the fly retuning.