Daily Assistance Work
Each day, choose one exercise from each of the three categories below, and do 50 - 100 reps of it. The number of sets you use to accomplish this is not important. You can do all of your reps for each category one at a time, or to finish your workout faster, you can cycle through a set from each category in a circuit.
If you chose a bodyweight exercise and cannot complete at least 50 reps, you can choose a second exercise to finish the total out. If you chose a weighted exercise and cannot complete at least 50 reps, you chose a weight that was too high.
Push
Dips
Pushups
Flat or incline dumbbell bench press
Dumbbell overhead press
Triceps extensions / pushdowns
Pull
Chinups / Pullups
Inverted Rows
Any form of dumbbell, cable, or machine row
Face pulls
Band pull-aparts
Lat pulldowns
Curls
Single Leg / Core
Any ab / core exercise
Back Raises
Reverse Hyperextensions
Lunges
Step Ups
Bulgarian One-Leg Squats
Kettlebell Snatches
Kettlebell Swings
Rest Between Sets
Jim Wendler does not provide any guidelines for rest between sets, so you can tailor this to your recovery and scheduling needs. Most commonly, rest times are kept between 1.5-2 minutes between sets. Some additional considerations:
You can generally use shorter rest times between your FSL sets, as well as your accessory work.
Longer rest times will generally allow for greater performance in future sets.
Shorter rest times will help build work capacity.
Off Days
You should get in some form of light cardio or conditioning on at least one of the days you are not lifting. As Jim Wendler says in the article, though, don't run yourself into the ground. If you find yourself struggling with energy, recovery, or your lifting, dial down the intensity of the work you're doing on your off days. It is also fine to spend a few weeks ramping up and add days over time.
Progression
At the end of each three week cycle, add weight to the Training Max of your lifts:
Add 5lbs to Bench Press and Overhead Press.
Add 10lbs to Squat and Deadlift.
You add the same amount of weight to your Training Max no matter how many reps you hit on your AMRAP sets. Never more.
It is also recommended that you follow a "five forward, three back" scheme for your TM - After you have added weight five times, reduce your TMs by three times their progression amount (15lbs / 30lbs) and then continue adding as normal. The principle behind this is "Deload before you have to deload" - Periodically deload a little bit on purpose, so that you are not forced to deload a lot (or take a break from your training) by hitting a point of overreaching or injury. Remember - Your Training Max is not a measure of your progress or your strength.
Stalling / Missing Reps
At some point as you're running this program, you may reach a point where you are unable to complete the sets and reps for your main lifts, either at all or with clean, fast reps. When this happens, it is important to remember:
You may have just had a bad day, so don't worry if it happens once or twice.
It is an expected event in the process of training and getting stronger.
It is not necessarily a reason to question, re-evaluate, or significantly change your training.
If you find that you are consistently not hitting the sets and reps for a lift over a period of at least one full three week cycle, it is time to lower your Training Max for that lift. The general guideline for this is to reduce it by three cycle increments (15lbs / 30lbs). If you find yourself feeling discouraged by this, again, remember - Your Training Max is not a measure of your progress or your strength. You will continue to make progress and set rep PRs on the AMRAP sets after you deload.
Reducing Workout Time
If you find your workouts running longer than you'd like, besides manipulating rest times, here are some other strategies you can use to complete the workout faster:
Use the rest periods between sets of your main lifts to complete accessory work. This has the added benefit of helping to build your work capacity by increasing training density. If you do, you should choose an accessory that will not interfere with the main lift you are currently performing. (Ex: Squats + Face Pulls, Bench + Ab Wheels, Deadlifts + Curls, etc)
Do a single set your Push, Pull, and Single Leg / Core exercises back-to-back. Rest anywhere from 1 to 3 minutes, and then repeat until you've hit your goal reps. (Ex: Push -> Pull -> SL/Core -> Rest -> Repeat)
Do the same as above, except instead of back to back, rest from 30 seconds to 1 minute between each set. (Ex: Push -> Rest -> Pull -> Rest -> SL/Core -> Rest -> Repeat)