A dockmate a few years ago left his down and the next time he was on the bay the engine overheated.
Towing pontoon motor up or down. Because of the intricacies of the trailer rails most toon trailers place the carpeted bunks for the pontoons atop the rails which jacks the boat up higher than a conventional boat. But he clearance issue good point about backing makes it risky. Back the boat down the ramp until the stern begins to float and the engine outdrive s are sufficiently submerged to pick up cooling water.
After tilting up the motor the intake vents were clogged by zebra mussels. Because pontoon boats are not fast people often overcompensate with large motors or even more than one motor. Leave enough space between trailer and vehicle for tight right turns.
If the motor cannot be trailered in the normal running position use an additional support device to secure it in the tilt position. We dont always have that option but realize that wind can push a towed vessel off course so you have to maneuver the towing vessel accordingly. The 70hp four stroke Evinrude manual like the Mercury manual referenced above says clearly not to tow the boat in with the motor in the fully up position.
You need to check with your states speed and weight limits for trailers first. Towing a boat long distances introduces new factors into the haul. Check your tires all of them.
Despite their large size and perceived sluggishness you can ski behind a pontoon boat. 3 Pontoons sit high. With a conventional boat its possible to turn so the trailer is almost 80 degrees from the tow vehicle but not with a pontoon on a trailer so dont get bitten.
You will also want to make sure that you take down the top of the pontoon in high winds. Ive got the new style low float on trailer with only about 2 inches of clearance when the motor is fully down on the Montauk. Yes you can ski behind most pontoon boats but your engine must be 70 horsepower at a minimum.