If you're going to put in a new tranny, see about getting a manual. They're better on gas and more reliable in our cars, as far as I've seen.
The cluster can be replaced, just buy any cluster off eBay from a 00-05 Neon and it will fit. Even the SRT-4 cluster!
As far as the 2003 motor goes, technically, it's supposed to swap over. However, due to the change in computer system between 2002 and 2003, I think a few of the sensors are in different locations, and might use different connectors. It would be a lot easier to swap a 00-02 motor into it. However, someone correct me if I'm wrong.
As far as the radio goes, just get an aftermarket head unit. The speakers in our cars are great, and it's really easy to install a head unit. Of course, if you really want a stock head unit that works, I can sell you my old one for $50, but then again it's still better to get one from Wal-Mart for the same price.