You can see all the colors under List of Genes. On the right side there is a column named Frequency it shows kinda how rare the colors are.
For the items, there is no existing chart which tells you how rare something is, but you will learn it with time. The rarest items are the ones you need for higher lvl buildings (some blueprints, Spirit in a jar, ...) other rare items are some of the Premium shop and items you can only get during events. Uncommen items are in example magic fruits, mutagenes, gray jar, they are not so easy to get, but still not as hard as other items. Vermillion is easy to get, but you need a lot of to research genes so they are also wanted and expensive. The items you can get with golems are common. Soapshroom, Hops and some others are uncommon - rare, but I think you need them just for the Inn (I might be wrong, not sure if you need them for something else :<)
It is hard to list all of the items and order them in groups, but it would be good to have a guide for this subject. If I find time and a little help I will write something.
For your last question you should visit the Premium Shop and hover over the items to read the explanation, there are a few items that speed up processes.
I hope I could help you anyhow :<