You wouldn't use the past perfect with that idiom in the past tense. You want to make sure the tenses match, "He had enough problems as it was."
It's slightly awkward phrasing, though. Remember just because you can legally make a sentence in English (or of course any language), doesn't mean it's the best way to say what you want to say.
It's hard out of context to say exactly how to say it better, but for example, "John didn't want to start a fight with Maria -- he had enough problems (as it was) and didn't need to add another." Here "as it was" is fine, and if that sounds natural to you then roll with it. Personally, I'd write something like "he didn't need to add to his current list of problems" ... but, the more I think about it, the more "as it was" seems fine.