The newer models are made with a newer mask, meaning they draw less power, generate less heat and should be more overclockable. Most people say they get warm but not hot to the touch, even without a heat sink. Since I want to run mine at 50 MHz 24/7/365, I want the coolest, most stable one possible.

Paralel: Yes, you can. They're cheap, too:

http://www.ebay.com/itm/MMPN-C68040FE25-Manufacturer-MOTOROLA-Encapsulation-QFP-32-BIT-W-CACHE-MMU-/181813260936?hash=item2a54ea3288:g:x5UAAOSwT6pVkfVg

Make sure you get an MC68040FE without a "V" at the end. The "V" signifies a 3.3 volt chip instead of 5 volts. You'll have to find someone who can desolder and resolder a 184 pin QFP chip.