After a whole lot of research, I think that I have achieved an answer, but I couldn't get my hands on any pearls so I don't have any experimental evidence. Most of it is based on messing around with tapioca flour, but I think it should carry over.
Anyway, the difference between traditional and instant pearls is merely the amount of processing they receive before they hit your hands, much like the difference between oats and quick oats. Instant pearls are cooked much farther than traditional pearls so I don't think you really need to invest in them.
Tapioca is a high starch, low protein ingredient so to make it softer we just need to cook it longer. Be careful though, as overcooking is going to result in a terrible mushy mess. Also, just like high starch sushi rice, rinsing will probably be a good idea, although I think it should be done after the initial boil and soak. The rinse should knock off the excess starch from the pearls, which I think is what is creating that tough skin when placed in cold liquid. You should rinse after cooking, in warm water, till the water runs clear.
The recipes I found on the internet were mostly split on the subject of stirring, but I think it's a bad idea (except to prevent the pearls from sticking to each other) as all it could serve to do is break starch off the pearls which is not what we are trying to do (save the stirring for when you want to use them as a thickening agent).
Anyway, I have some on order but they aren't getting here for a bit. I'll update once I get to play around with them.