I think that if an algorithm requires access to individual elements of the piddles, rather than being able to apply single operations to whole piddles at a time, there is little to be gained. What you might gain from more efficient duplication, you lose by having to call one or two functions per element during calculation or conditional testing.

From my very limited understanding of the OPs problem, much of the effort involved in the algorithm involves:

• interchanging whole rows & whole columns in 2D arrays.

  I don't think that PDL is particularly efficient at performing these operations, especially the latter.

• performing "bit-wise" boolean operations and 'counting-the-set-bits', on pairs of rows of zeros and ones.

  If the rows of 0s and 1s were encoded as simple bit-vectors, then not only can standard Perl can perform both these operations more efficiently than PDL, the storage requirements are 8x less.

I'd be very happy to be wrong here, but I just don't think PDL suits these particular types of operations.