In the sentence, "All I had, and all I have now, were clues", should the verb be "were" or "are", or should the sentence be rephrased so that I don't have to choose between matching the verb to the past tense indicated by the first part of the sentence or the present tense indicated by the part between the commas?
There two clauses here, All I had were clues and All I have now [are] clues, and the attempt to bring them together in a single sentence creates a problem of agreement. Many readers might pass over it without noticing the inconsistency of the tenses, and if you think that may be true of your readers, then you might want to leave it as it is. If you don’t think that, you have to rewrite it, as, for example Clues were all I had, and clues are all that I have now.
I'd consider the version "All (that) I had, and all (that) I have now, were clues" to be fine for my AmE ear.
It would be similar in meaning to "Clues were all (that) I had, and all (that) I have now"; except that in the original version, the expression "and all I have now" would be treated as a supplementation.