So my original answer was incorrect. "Hope this helps!" is a declarative, not an imperative. Instead of deleting my answer, I think it might be helpful to explain why I should have known it wasn't an imperative, and pull out the bits from the original that were correct.
Imperative clauses are usually in the second person, like:
"Hope for the best!" (You should hope for the best.)
A declarative clause is just a statement, like:
"I am editing my answer." or,
"Hope this helps!"
The second person and first person form of hope are the same, so I got a little confused because I didn't think about it carefully. I should have been able to tell that the clause wasn't an imperative because an imperative is usually a command directed at another person, and "Hope this helps!" is stating something in the first person.
I would expand "Hope this helps!" this way:
I hope this (answer) helps you.
You would say "This answer helps me." and not "This answer help me." because the subject of "help" is third person singular. So, "Hope this helps (you)!" is OK, but "Hope this help (you)!" has a verb agreement problem.
In your suggested sentence, which is grammatical, you changed the wish from the present (helps) to the future (will help). This is OK, but it's not exactly what the original author expressed.
Well is the "adverb form" of good, and good is an adjective. People in live speech mix these up all the time, though.
Adjectives can follow the verb to be, to feel, to seem, and a few other verbs, because these types of verbs take complements.
For example, you can say "I am hot" or "I feel sick." In these situations you can use good. You can also use well (e.g. "I am not well.") since a meaning of well when it is used as an adjective is "not sick."
Well as an adjective is not often used outside of a verb's complement. For example, it would be far more usual to say "I'm about the release all the patients that are well" than "I'm about to release all the well patients."
This contrived example might help illustrate also:
A: Did you test all the tools?
B: I did, each one is good. (You cannot say well here because tools are not a thing that get sick)
A: Well, give me one of those good tools. I need one. (Etc.)
Best Answer
The reason this sentence is confusing is the ambiguous "it is". Depending on what the listener believes you are referring to, the sentence may take on different meanings.
In this case, "rain" is a quote about the weather. Since it is a quote, it does not have a tense and is correct.
Now we are talking about an action that the sky is taking - it has rained, it will rain, or it is raining. Since we are talking about a state that the sky will be in for some time, we say "it rains".
The reason that the first sentence ("if it is rain") sounds wrong to a native speaker is that they are assuming rain is a verb associated with "it" and thus should be conjugated as such.