1) What he meant (had) remained unclear. Both simple past and past perfect are possible, but the past perfect needs extra context to justify it (it is not justified by this sentence alone). Note, no comma.
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Silvia Black"Whatever they suggest" will be an adverbial clause of concession, right?Yes, I think so.
Silvia BlackHow should I paraphrase the sentence to make "Whatever they suggest" - a subject or an object clause?Whatever they suggest will be carefully considered.