Like many terms between English and Mandarin, the translations and usage are not always easy to explain, but I'll try my best.
1) 能, generally speaking, means the same thing as "may" or "can" when "can" is used for permission. For example, 你能帮助哦忙吗？ means "Can you help me?" In this case, permission is already granted for the listener to help, and "can" doesn't automatically imply "have the ability to." 会 though means "to know how to" or "will do." When someone uses 会，it means he/she absolutely has the ability to and/or will do something. For instance, 我会说汉语 means "I know how to speak Chinese," and 我会把车修好的 means "I will definitely get the car fixed." When usage applies to ability, both mean "able to," but 能 does not automatically mean "definitely have the ability to," whereas 会 does (in other words, 会 is absolutely certain whereas 能 is not).
2) 显然 is usually used as an adverb and 清楚 is usually used as an adjective (although they still can cross over). Specifically speaking, 显然 comes into use when something becomes visibly clear over time. For example, 我调查过后，最后结果显然出来了 means "After I investigated, the final result became clear." 清楚 though can be immediate. For example, 我看得不太清楚 means "I can't see it very clearly."
3) 来 means "to come" in any context. 哥哥来到了姐姐的家 means "elder brother came to elder sister's home." 过来 however is usually only used to mean "come to me." 你明天准备过来吗？ means "Are you planning to come over tomorrow?" 过来 can also be part of in certain specific terms: 过来人 (literally "come over people") means people who experienced the past and are still alive to talk about it.
I hope this helps. Please let me know if you explanations confuse you.