There were only 300 or so Merlin 61 Spitfire F.Mk IXs built. I am talking about contemporary fighters. The Me410 also entered service in 1943, correct? So, like the Spitfire LF.Mk VIII and Spitfire LF.Mk IX, by far the most common version of each mark, the Me410's service life would be overlapping with the Merlin 66 Spitfires, not so much the Merlin 61 Spitfires.
As to the first Spitfire Mk VIIIs using the Merlin 61, no. By the time the Spitfire Mk VIII was coming off the lines the engine put into it could have been a Merlin 61/63, Merlin 66 or Merlin 70, depending on its intended role. They were all produced concurrently, though the Merlin 61/63 was not continued with for long.