Another thing I think can be a good practice that I haven't gotten the chance to do myself is to try and sit down, build as good decks as you can with your cube and then playtest those. That way you can get some insight in what some raw gameplay is actually going to be like, and get a feel for what cards does or doesn't contribute to whatever it is you want to get going.
For example, let's say you've got the riptide style aggro package of recursive black (gravecrawler, bloodghast etc), human weenies and the like. You also want to do something about your control decks, since they feel lacking. Build as good as a representation of the aggressive decks as you can, and then build "drafty" control decks to beat those! Only when you've got a control list that really feels good against the aggro decks (or whatever gauntlet deck you're building) do you move forward with incorporating it into the main list.
When building the "deck under test", that you're pitting against your cube gauntlet, I'd suggest feeling free to try whatever cards you have lying around. Try to stick to singleton and simulate something that looks like it's actually been drafted, but otherwise feel free to do whatever you want.
The reason I'm bringing this up is, when doing such a big overhaul I think it's easy to get stuck in an idea of what the cube should become after you're done, and then running the risk of getting disappointed when it turns out you're still ending up with the problems you had before.
Ultimately you want to build a cube that has really great gameplay, and I think playtesting the decks you actually want people to end up drafting is a good way to start in the right end, namely the actual magic games. The drafting can then be a layer that comes in after you have some playtesting done, where you actually know things about the format and can make judgement calls based on something more solid than just mere speculation.
- Don't draft your own cube all the time. When you draft other people's cubes, you break the monotony of playing the same cards over and over again. You might play with and like cards that you hadn't even considered yourself, and use this inspiration to spice up your own cube.
I think this is sound advice, and to reconnect with the stuff I wrote about above, why not look at other draft formats (cubes or retail) and build decks from those and play test? Ask a friend to join you in just battling out with some decks, either in paper or on some online client, and really get a feel for different drafts.