Be sure all the settings are correct, such as resolution, interlace, etc. If it takes 4 hours for a 2-hour encode, it should only take 6 hours for a 3-hour encode.
Beyond that, know that CPU and hard drive speed are the two bottlenecks. RAM is barely used. Adding RAM does nothing.
You'd have to add a new high-end computer to up the encode speeds. I can get maybe 100fps MPEG-2 on my quad-core, in
MainConcept. That means a 2 hour video takes maybe 45 minutes.
You can always buy more computers, and
use a KVM!