1) There are several available ratios for Dana 44 gear sets. You'll probably want to move up to one of the following: 3.07, 3.23, 3.31, 3.42, 3.54, 3.73, or 3.92. Of course you'll want to pick a rear ratio based on your transmission ratios and the torque/HP curve of your engine. I have a 3.54 with my TKO600 and torquey FE. Post your specs and you'll get some suggestions on what ratio to go with.
2) I'm not sure I understand -- are you talking about this connection from the primaries to the side pipes?
3) Any good Corvette body guy should be able to handle that problem.