One option you have is to use Book Designer to convert all the mess you have and then you'll have them in Book Designer format which you can then use to convert them into LRF, PRC, PDB, LIT, and any other format supported for output.
As for the best reader for Windows there are two camps. One says MS Reader is the best and the other says uBook is the best. I personally prefer MS Reader. But then, I have not tried uBook in a very long time. So give it a good as well and make your own choice. Then you can generate books to work with the one you like best. But if you do decide to go with MS Reader format, you will need to have Word and the addin to generate LIT. The add-on is free from Microsoft.