I have two of those with single cylinder Briggs. I can't help with the electric PTO, the single cylinder PTOs are mechanical. As for the tiller driveshaft problem, you may have the wrong drop box. The twin series is similar in construction and attachments to the S series that preceded it. I have never had two of these tractors next to each other, but I suspect the Twin cylinder tractors may be longer and that you may have a drop box for an S series.
The warning means to turn off the PTO to the tiller before you push in the transmission clutch. The reason is, if the tiller is still in the ground, it will continue to push the tractor and could cause tiller driveshaft or gearbox failure. The driveshaft could twist or the chain could break in the tiller gear box if allowed to push the tractor. You don't want to break stuff on this tractor, as parts are nearly impossible to find. Word of warning, the tractor will not steer well with the tiller in the ground, so point it in a straight line before putting the tiller in the ground.
These are great tractors, and an overlooked brand. I hope yours has hydro lift, as the tiller is a bear to lift.