Definity check out palmers like stock said it's online and free, read it all, it's good stuff. Getting a better idea of the basics will clear up a bunch of stuff with your process. I get the idea that you might be doing a few things less than ideal just from the efficency.
Plenty of ways to sanitize. I personally do an initial cleaning removing labels and other junk followered by baking the bottles at 350 to turn anything living into ash, warm up slowly if you bake them or they can crack. Then Star San before bottling, prolly overkill but I'm happy with it. As for starters invest 20-30 in a homemade one plenty of diy instructions online. I use an old coffee pot for my flask.
Now to figure out some stuff so we can clear up with what your telling us.
Did you boil your either the sugar or honey addition?
Is your equipment big enough to handle 5 gal grain bills? What equipment do you have?
Did you pour your boiled wort onto ice or was your container in an ice bath?