Would you be willing to maybe print out the weights for each layer? I'd be interested to see what features your conv net is capturing.
The plan is to operate on 32x32 data for now, then try scaling up the input images or just scaling to 512x512 to see how input data size/resolution affects the DeCAF/pylearn2 classification result, either positively or negatively.
As far as network weights, I haven't tried to print/plot the DeCAF weights yet (though there are images in the DeCAF paper itself). For pure pylearn2 networks, there is a neat utility called show_weights.py in pylearn2/scripts.
Another method, which does do "chopping" is http://www.stanford.edu/~acoates/papers/coatesng_nntot2012.p... - which is a little different than what I am currently trying.