I'll offer my 2 cents for what it's worth.
JK said it well, we'd need more info on your logs, but also on your condition (age, weight, height, other physical activities, previous injuries etc.)
So you have been at it for 2 years and you can do L5D2 (without breaks in the middle of sets!) but you can't beat the 5 minutes on L2D3? So on D2 you do a total of 25 pull ups, 75 push ups and 130 squats, but you can't do 13 pull ups, 26 push ups and 26 squats under 5 min? Sounds odd... We'd really have to know more about your logs, as JK pointed out.
The only way I see that being possible is if you take lots of breaks on D1 and D2. In that case, your progression is not really working as it should, because you're not developing enough strenght and stamina to beat L2D3, which should be a relatively easy stage.
I believe D1 can be misleading, because if you take lots of breaks between and mid-sets, you could be doing L8D1 for 2 rounds in 20 min! hehehe
I guess you shouldn't progress levels if you can't beat D3. On the other hand, maybe you feel more motivated this way, and if that helps you work out regularly and stick to the program, more power to you! Simplefit is a program, not a law! Also, you may be a senior, or have previous injuries that hinder your ability to progress above certain levels, in which case you should consider those limitations.
The important thing is to keep at it. Any workout is better than no workout!