if i'm not mistaken, clonedvd is a single pass transcode, which means that it only "goes through" the movie once and while it's going through that pass, it's transcoding, trying to distribute bits as it deams necessary based on the constraint of 4.7GB for the movie.
Because of the space constraint, going through at LEAST a second pass (DVD shrink's "Deep Analysis" option) will make a significant improvement in quality, but as a result, it will take longer...
If you're like me, you'll go through a maximum of 10 passes using CCE, which explains why it takes that much longer.
As for DVD shrink's AEC option, I would choose to use "Maximum Smoothness" which tends to reduce blockiness in the movie at the cost of making things not as sharp. you could choose one of the other options ("Maximum Sharpness") but you'd get more blocks.
I strongly recommend using something that has a "Deep Analysis" option in it. It'll make a big difference in quality and it'll take only about 2X as long. You might not notice the quality difference now, but if you watch your movie on some higher end equipment, it'll start to bother you.