Hey, Spanks, pretty amazing you are shooting for a few hundred peppers! Cool. But it is tough to generalize some answers because it depends on your lights, your growing medium, where you are now, and how you plan to procede.
For starters, it would help to post pictures of the 'sick' test plants, what you did leading to that point. If you are already pretty sure you over-fertilized, then cut back on the next batch. Many go with a "1/4 strength" rule of thumb for seedling nutes. Very easy to exceed! More is not better. While in small pots, the peppers like a light, fluffy medium that drains well. Bottom watering is great.
Everyone's 'pot up' plan is a little different. I've noticed many start with 72-cell per flat, then move each of those up to (about) 4-inch, then move up to a gallon, then move up to 5-gallon or straight in the ground. But it is only one of many ways.
Good luck and do enjoy the 'search' feature. Also, the new "GLogs" forum sometimes has some real nuggets of info at the beginning of each Glog. You'll get some good ideas (sometimes) there. Pick your favorite players and feel free to pester them directly. Have fun....