You say you're in 16:00 flat shape...is that verified by a recent race? Also I think you answered your own question in your first post by saying you haven't run the fast stuff, therefore it's going to feel hard.
Did you do the 200s after the 3 sets of 3x400? If so it will feel harder. I actually did this workout last week four days prior to my race (I think you posted a similar thread awhile back with this workout and I used it) . I hadn't really done much speed stuff (yes as we age, 200/400 is speed work for us) and I struggled with it at first but got through the workout. The 400s I got faster with each and by the time I did the 200s it was hard. I still did fine in the race. Could I have done better? Sure if I actually followed a continuous plan. I think doing the 200s helped me to have a fast finish in the race. But I agree with others if you want to get faster you have to do more speed work, I just have to be careful not do too many of them or I will get injured.
Trust in your training plan if you're following one. Good luck.