The beauty and downfall of percussion notation, is that you can do whatever works best for you. The problem is that not everyone will understand what you did. For this very reason, and legend (a staff legend) preceding or following the music will be a must. But as far as changing the toms to pads… there is nothing wrong with this, and is quite acceptable (my opinion of course).
And as your last point, I would certainly create a new flow, and use that as the legend.
As far as your playback concern. For me, I would just use the tom playback. But each person is different, and you should figure out what works best for you.
I’d love to see to the transcription when you are done, if you aren’t afraid to share it.
Robby