Pigpen stayed offstage for most of the acoustic sets I think (then they'd have to call him back on for his one song). But there are lots of exceptions -
just at random - he plays organ in the acoustic Black Peter 2-23-70
& harmonica in some New Speedways (for instance, the one in Festival Express)
& piano in the New Speedway Boogie 6-13-70
& piano for a whole bunch of songs on Aug 18 & 19.
Overall, in the early acoustic sets he's not there much, but later on in the year, he found more things to do in the acoustic songs.