Go with an M44. There are significant differences between the electrical systems. For instance, none of the M42's have a MAF (all are the flap-type AFM), among other differences.
If you really wanted to get the best of both worlds I'd use parts from both. I strongly suspect it can be made to work, but I'd go for the M44 if you're looking for plug-n-play.
You could use an earlier M42 if you swapped out the entire harness as well, but that raises legal problems...our mechanics in PA would cite the missing OBDII as a safety & emissions inspection fail. Our DOT isn't even that strict, can't imagine what it'd be like in CA...