THINK OUT is not really a normal phrase or collocation. Do you mean THINK OF?

"Come up with" means to create or produce something, e.g. a plan, a process, an excuse (sometimes with the implication that it is done under pressure). For example, "She came up with a new process for smelting iron" or "he's always coming up with excuses not to do his homework". "Think out" means think about all the effects of or problems with something. For example, "He never thinks out his ideas" or "the plan was not well thought out". As the examples above so, the meanings of these expressions are different and you can't substitute one for the other.