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The owner's manual you cite, shows that Whaler states the trolling motor position is to be on the starboard side. That they reinforced it for that purpose. Yet, we see many trolling motors (kickers) mounted on the port side. Port side makes more sense in my case, considering I have the superb Super Sport Limited model.

If I add a kicker/aux/trolling motor, it will likely be on the port side. In my case, I'm looking for an 8-9.9 two stoke for lighter weight, as my Johnson/Suzuki 90 is a bit portly.

Concerning the original poster's issue; I know of a few folks who use the "sail" edition of kickers quite successfully. Usually because having the prop that much lower is beneficial in rougher waters, much less likely to catch air in the chop. They also have a "high thrust" prop, and battery charging capability.
The extra weight is minimal, perhaps 2-4 lb for the extra length. That shouldn't be a deal breaker.

Keep in mind, the powerhead is the heavier part in a 4-stroke. The lower units should be fundamentally the same weight.