How stay fit enough to make moderately hard rides a couple times a month?
The difficulty is you want specifically to train for endurance, but you want to do it in short bursts.  

I'm not saying a few squats won't help a bit, but they won't do the job.  And trying to push too hard on a bike for a few tens of minutes might improve your aerobic capacity but quite possibly at the expense of your knees.  You also need to be in a similar geometry so the benefit of an hour or 2 of moderate pedalling on the recumbent while reading/watching TV will be limited.  However (almost) within your constraints that might be the best place to start.  Or drop the elliptical in favour of more bike time if you really don't want to increase your total time.

That's the fitness aspect; the soreness will only be dealt with by time in that saddle, or one very similar.  If the saddle suits you you don't need ages in it to keep yourself at a level suitable for spending 3 hours on it, but you do need to get on it every few days at least.

Anything you only do a couple of times a month will be hard, skipping anything over a week or two really hits your fitnesss for a specific task (a shorter figure even than that is often quoted, but in the context of an athlete's peak performance rather than something more casual).

I'd also suggest that particularly as you build up the long towing rides rather than walking at the end you take a decent break and ride again.  This will be tricky if there are uphills involved, in that case you might get away with a walk or 2 earlier in the trip.

One further suggestion given comments and other answers: switch one of your mixed exercise sessions per week to bike only from a month before your first ride/paddle trip to a week before your last of the season.