So, just started using Ubooquity yesterday and I think its an amazing product. Just out of curiosity, is there a reason you're not using Readium for displaying epubs? Its open source and handles fixed layout and reflowable epubs really well:
I think Readium-2 supports CBZ as well. It doesn't support PDF, but maybe you could just check the extension and switch to readium for epubs and use your existing reader for PDFs. Just an idea, again love the product, keep up the good work!
Customer support service by UserEcho