Well it says it needs to be cleaned out before 12 hours of the mix being in there or it's screwed, and I have gotten a good majority out but it's so small that I cant fit much in there to clean it all out, is there any secrets to do so?
Castrol’s purple stuff with room temp water and 10-15 seconds of shaking work well. Putting 3-4 small steel balls from a ball-bearing in the bottle helps a little. I don’t think that it’s necessary to get the bottles absolutely clean.
Replacement bottles are widely available, or on-line at the Container Store.
Rather than using the ZFX mixing bottle, try a 35 mL oral syringe. They're the perfect size for mixing up 1/2 or 3/4 oz., the small tip allows you great control of how much Z ends up on your applicator, and you can get every last drop out of the syringe. See this thread for a little more info, or a search on "syringe" will turn up quite a few hits for you.