For hoots and giggles I went ahead and did a by State PR using the largest remainder method and the Presidential Vote. That would for the 111th Congress have given a House with 233 Democrats 201 Republicans and 1 Peace and Freedomer (from California of course).
Also, your PR calculations for the House are interesting - how'd you figure them? I'm surprised by those numbers - since Democrats won the House popular vote by, I believe, 8 points, I'd figure they'd have a larger majority.
I already said how I did it. I used the Presidential vote rather than the House vote since there are a number of districts where there was only token opposition if any. BTW, using the National Presidential vote and allocating vis the largest remainder method yields 230 Democrats, 199 Republicans, 2 Naderites, 2 Libertarians, 1 Constitution, and 1 Green, so the effect of using 50 constituencies instead of one big one was minimal as far as the big parties were concerned.
Doing that with the House vote yields (once one eliminates all votes for independents and write-ins for convenience's sake) 233 Democrats, 194 Republicans, 4 Libertarians, 2 Green, 1 Constitition, and 1 Independence using the largest remainder method.