The dollar sign is the prompt that is already there, don't put that in. I thought the post you mentioned was saying the the old node-red version was likely to be the problem.
I think you would probably be best just to run the pi install script to get a consistent set of everything. The advice not to upgrade was, I guess, just after the new node-red was released, at which point there were a few teething difficulties. I have upgraded all my systems without a single problem.
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