Are you running the two jackshafts for more reduction like a tote gote? I was going to say run the second jack higher up like a tote until you said low seat. Hmmm. Low seat as in just above the rear tire?
Just thinking out loud here, how about two shorter jacks. First one off the driven to the first cog which would be under/just behind the cylinder, give or take, and the second just behind it going to the final drive sprocket. If it was just a 10/20 sprocket reduction under the cylinder, that would not take much room. Shafts 4" apart give or take. More reduction, farther apart, space limited.... This would also put the sprocket on the other side....
But even so, it looks like plenty of room now with two full length jacks. Must be planning on a lot of reduction....