First thing I would try to shoot more crystals. Easy way out. I once struggled 
with a 2.7A data set for weeks only to find out I had a 1.5A diffracting 
crystal taking a bath in some storage buffer right next to my bench. 
You mention you have at this point you are looking at 25% rotamer outliers. I 
wonder if at 3.2A if you really have density for these side chains. You may be 
trying to fit these side chains in very weak unreliable (e.g. noise) electron 
density. As Ed Pozharski suggested, omitting these may be the right thing to do.
How certain are you of your space group and how did you generate you Rfree test 
set. You should have Rwork>Rfree after refining your model.
HTH
Yuri 

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