Hi Andrew, I'll take a shot at this as your question encompasses a lot of ground. I think the best advice I can give you is that setting up a shop to make pens is difficult to do "on the cheap". Sure, you could buy a cheap lathe, cheap chisels, cheap dust management, etc. but in the long run that is actually going to cost you more money. If you do stay in this hobby for long, you will discover all the limitations, less than desirable attributes, etc. of the equipment you spent your money on and end up being less than happy with it or replacing it.
It would help us to know what shop equipment you have already and if you anticipate making other items outside of pens that you could spread your equipment investment over such as other turned items like bowls, bottle stoppers, or other things people like to make such as cutting boards, etc.
As far as organization of the pen kits, i bought the below Sterilite boxes / bins from Amazon.
They have worked well for me as I can store, depending on the kit, dozens of any particular pen kit along with the required bushings and drill bit(s). As you may have discovered, some pen kits use the same drill bit(s) and or bushings, so this can result in some duplication of bits and or bushing sets. However, for or me this is not an issue as the added cost to me is minimal and I prefer the simplicity of pulling out a bin and having everything I need to make a pen (minus the blank) in a single container. I have a lot of different pen kits (I'm not saying how many lol), so for me they keep me well-organized. They also work great to hold the blanks and I have put 50 plus wood / acrylic blanks in a bin. The bins are stackable so they don't take up a bunch of space either.
This storage system may or may not work for you personally, however. I think many people start off with one type of a system and migrate to another once they discover the best workflow for them based on quantity of pens they make, frequency of their pen making, how well organized they are personally, etc. As you ask questions in this forum, you will quickly find out there is not one "best way" to do any part of the pen making process. The "best way" is actually what works consistently best for you and that often requires some experimentation and outlay of time and money.
A final comment would be when seeking advice, please give us more information on where you are starting from equipment wise as well as skill set, budget, etc. One person may think cheap is $10,000, and another might be more like $1,000. Let us also know what you wish to achieve, such as "I want to make about 50 pens a year for gifts for family and friends", etc. The more information you can give us on your situation, the better the advice will be. Good luck on your journey....