The fact that he's been exposed in a way to a stray may be enough to trigger the "dominance" issue. Since he is grooming the kitten all will more than likely be well. I would definitely keep a separation at times where you cannot intervene quickly in case something goes wrong. However, if the cat has not shown any signs of agression in a month or so, things will probably be OK. From your description it sounds like he's not totally aggressive, but for safety's sake it is best to err on the best side.
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Smile, it will make them wonder what you are up to!

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