Now that the peppers are dry, you can separate most of the seed by placing the peppers in a large covered jar or can, and shaking vigorously. A large jar works best, so you can see how much seed has broken loose. Then pour the broken peppers & seed through a screen with holes just larger than the seed (a collander or strainer basket often works for me). This will catch most of the stems & debris. Then pour the seeds through a sieve or strainer with holes just smaller than the seeds (to remove dust & under-developed seeds). You might want to be outside, or under an exhaust fan, to do this.
If you intend to make pepper powder, having a few seeds left on the pepper pieces will increase the potency. Hopefully most of the stems will break off during the shaking.