You are right, let me be clear has the potential to sound forthright. As you suggested, let me explain more clearly is good. You could also say: Let me clarify / I will clarify / just to clear up any confusion...

"Let me be clear" is relatively strong. It can be neutral or irritated. Sometimes, the speaker is emphasizing the importance of some information. Example: Manager (neutral voice): "Let me be clear. Only authorized employees can access the confidential employee records. Unauthorized access is grounds for dismissal." Sometimes, the speaker is upset with someone's behavior or lack of understanding and the voice shows the irritation. Example: Manager: Due to the pandemic, everybody must wear a mask at work and stay two metres away from other workers. Worker: But masks are itchy. I don't like wearing them. Manager (annoyed): "Let me be clear. EVERYBODY must wear a mask at work."

This is a good question. I will often say "To be clear, ....." instead of "Let me be clear." For example, "To be clear, I had a good time at the birthday party, but I was tired." This is a more neutral way of saying the same thing.

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