The millennium was only made in a run of 1000, so it's well worth keeping it as good as you can. Unfortunately rust on the rear arches comes to all pumas so there's little you can do to avoid it unless you treat it well from new. The only sure fire way to get rid of the rust is to cut it out, then treat the inner arches as seen in this post:
http://www.projectpuma.com/viewtopic.php?p=15170#15170" onclick="window.open(this.href);return false;
£3K for a millennium is pretty cheap in todays market.
(As long as it's not been to the moon and back for mileage)
Be careful with the paintwork as it's not a metallic and therefore doesn't have a clear lacquer coat on top protecting it from the elements. It may have oxidised a bit over the years to go a bit dull and flat. Getting a paintwork restorer (like t-cut, but that's a bit harsh IMO) will remove the oxidation and bring back the shine.