The shaft arrangement in a Super 55/550 is backwards from the rest of the Olivers. The inner shaft runs the transmission, and the outer one is splined to the clutch cover, turning whenever the engine does, powering the PTO and hydraulics. When the outer shaft turns, only the gears in the very front of the transmission case should turn. The top gear powers the hydraulic pump, the bottom one powers the PTO. The shaft for the PTO goes through the middle of all the gears on the lower part of the transmission, so a bearing could be seized in there. That might explain why engine will only run with the clutch pedal down. If the PTO gear or shaft is seized inside the countershaft, it and the transmission are try to turn at 2 different speeds, but can't if they are welded together via a bad bearing.