If you're looking for a good program 2-3k without customization is realistic. Customized with multiple program capabilities (i.e. 4free sites and PPS/partnership in the same package) you're looking 5-7k range without batting an eye.
MPA2 is uneditable and Zend encoded, so you can't do anything to it without paying their rates, which in my opinion are unreasonably high.
www.groundbreak.com works fine for one site.
Haven't heard anything good or bad about X3. I know traphica is being used by Lightspeed and a few other medium sized players. That guy is always willing to cut deals. Just make sure the return emails on your affiliate mailings don't go to them. My two beans.