All his workouts should be done by feel. You will get used to them and in turn get faster.
Interval workouts should be about 4k effort, I like to cut down from 5k effort to close to 3k effort when I do them. Threshold varies from person to person based on your aerobic strength. You should also do these by feel - obviously threshold runs with short rest will be faster than a 20-30 minute tempo run with no breaks.
Rep workouts should be controlled and the jogs should be slow enough so that you can do the next rep at the same pace and effort. I usually don't have the guys do 800s at rep pace, since running at rep pace for more than 2 minutes is pretty tough. I usually modify it to 600s. These rep workouts are usually done from mile to 1200 pace and fell controlled, working on form and pace.
As for the easy runs, Daniel's chart shows the pace as you should run when not tired. Recovery runs are MEANT to be slower, and should also be done by feel. I run average 7:15 pace in base with ease, but in season I rarely get down there unless I've gone a few days without workouts. I also like to do most of my runs at a recovery pace and finish the last 2-3 miles at a faster pace, closer or faster than what Daniels says.
Keep in mind, you don't have to do 3 workouts just cause the schedule says. Sometimes doing 2 a week is better, especially if you replace a tempo with a progressive long run, or a rep workout with short fast sprints.
I'm a big fan of Kellogg, and I believe most workouts should be done by feel, except maybe during crunch time (last few races).