Looks like I may have found a function that addresses my needs. Bootcov in Design handles bootstrapping from clustered data and will save the coefficients. I'm not entirely sure it handles clusters the way I'd like, but I'm going through the code. If it doesn't, it looks easily re-writeable. As far as I can tell, boot in package boot would do clusters only if the estimation function passed to it pastes together data based on the clusters boot selects.
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