1. Try changing your Simplefit workout in reverse:
For example,
level one day one do
AMRAP 3 squats, 2 pushups, 1 pullup or even tougher do 3 pullups 2 pushups 1 squat (can apply to any level)
2. Try doing Crossfit's "Chelsea" but modifed the simplefit way:
Each minute on the minute for 30 minutes 5 pullups, 10 pushups, 15 squats on level 7 but level one would be 1 pullup, 2 pushups, 3 squats.
3. For day two attempt to complete each round faster than the last round. The goal here is purely speed of repetition while maintaining a strict form. Potentially rest time could be undefined so your just doing speed work. For example lets say I'm doing Level 1 day 2. First round of 2 pullups, 6 pushups, and 10 squats takes me 60 seconds to complete. Then rest for 3 minutes or fully recover. The 2nd set I want to beat 60 seconds. And so on.
4. One week change your program to burpee pullups. Your doing a pullup, pushup, and squat in one movement. So for day one level one AMRAP burpee pullups (I guarantee some fatigue on this one!

5. Do a heavy week or even a month of Simplefit with a 20 lbs vest or other substitute.
6. Change the type of pullup, pushup, and squat for your workout. i.e. do L-pullups or equivalent substitute, clapping pushups, dumbell weighted squats or even pistols.
7. Try a pyramid run of day one. 1st set would be day one level 1, 2nd set would be day one level 2, and so forth then go back down to one.

8. Try a 50 or 100 meter sprint after each round of Day 2. Rest the full 3 minutes and repeat.
9. Stuck on day 3? Try full failure rounds before moving on or resting. For example, Your PR on L1D3 (level 1, Day 3) is 7 minutes. Your max pullups are 4, max pushup is 18, max squat is 20. When doing the pullups make 3 genuine attempts at five pullups once you hit rep 4, if you get it make 3 genuine attempts at 6 pullups, etc. Granted Simplefit doesn't recommend going to failure but occasionally it might shake things up enough to push past the plateau.
10. You could even try a slog fest one day and attempt day 1,2, and 3 on the same day. Complete day one in the morning, then at noon do day 2, then in the evening do day 3. I don't recommend an all out gut busting workout on this either. Just a 60-70% intensity level. So if you can do 20 rounds of L1D1 maybe you only do 15. Save the push for the test in the evening and cruise through the first two workouts.
Ok that's it. Good luck!