We have been talking about this for a few days.
Check these threads for basic info and then read on.
http://www.thehotpep...-these-peppers/http://www.thehotpepper.com/topic/27853-ok-to-transplant/
I would recommend two things. 1, pot up to something that fits the requirement. What I mean is do not go from coffee filter to #1 pot. You are just asking for a loose root system. 2, wait until you have an established root system before potting up again.
With that being said, when you say that your plants were being blown over, do you mean that the pots were tipping, or the plant in the pot was tipping? You are in DE, which means you probably aren't hardening off until like Apr/May, how long were they in 6 oz cups? That may be a problem. If they were in a 6 oz cup, which you went from filter to cup the same time as this last year you are gonna run into a number of things. First, you are going to be route bound. i.e. the roots will continuously wrap themselves in circles around the inside of the cup and that makes it difficult to spread the roots once you pot up. Also, there can be physical issues that come with that. Second, you are gonna be really, really top heavy. A 6 oz cup with a 3 month plant is gonna look pretty funny, number 1, but you cannot counter the size of the plant with a tiny cup.
I think you should be fine with either a 6 oz, or the 2.5x3 pots from the filter. However sticking them in a seed tray (like a 72 cell or 50 cell) and waiting for a few sets of true leaves and an established root system cant hurt. Then, you need to make another move. 2.5X3 is going to be too small for a 12 week old plant. You are gonna get root bound.