Long type motors are made for guns with certain mechbox designs(m series, I think the 249uses one, there's one more buri forget , it's weird like maybe the P90. It's one that looks like it shouldn't have one. The short motors are used for every other gun on the market. Basically it all depends on where your gears sit, and how far away they sit from the motor housing. I don't think ones better than the other. I just think the long motor's pinnion is attached to a longer rotation gear.
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