@TimRuffing
in your paper you say that the change can also be shuffled, but I do not see how it can avoid being correlated due to the specific amount of the change relative to the input. What I have done is separate the outputs into the shuffled amounts and change amounts and treat the change outputs at just one step above the normal unspents.
I also think that to be using specific shuffled change outputs in future shuffles will contaminate things, so while it is a bit better than the transparent unspents, it is nowhere near as private as the shuffled amounts (assuming all the shuffled outputs in a round are the same value)
By allowing shuffle rounds to happen every minute, it will be possible to reshuffle already shuffled outputs and the wallet can track how many shuffles (and participants) each unspent has gone through to create a privacy metric.
James