Click in each photo for a larger version
If you want to get across bodies of water like this .......
.... and like this .........

(as I plan on running the entire length of the texas coast line, encountering numerous bays, cuts, channels and jetties)
then you need a boat!

I've also considered using a pair of kayaks see here

Using class 4 white water rafting tubes and a custom frame to allow a motorcycle tire rail, you have a drive on then drive off ability.
Since the motorcycle already has an engine and rear wheel drive, use that to power a set of rollers to drive a prop. A paddle or oar can supply the rudder effect for steering.

A tarp can be put down on the tire platform and the bike ran over it. Then the sides of the tarp can be lifted up and secured to the tube, keeping the bikes tires from getting any saltwater wave spray.
The front wheel assembly and rear wheel assembly clam shell together, holding the tubes, spars, oars and/or paddle, loading ramp, etc. One side gets hitched to the bike and the other holds the trailering wheels.

Two people make the trip across, one stays and the other rows back to pick up the next bike and rider.

When the boat is not being used as a motorcycle ferry, other frame sections can be installed with the aft section fitted with an outboard motor mount, then the boat can use used as an (almost) conventional runabout boat.

Rigged for scuba diving, the front spray platform can be lowered into the water a foot or so and be a swim up platform and an easy step up into the boat.

bike ferry requirements:

1) carry one or two bikes, or one quad, or one sandrail
(possibly a "side-by-side" as well)
though all vehicles will be street legal

2) drive on / drive off

3) propulsion system:
able to be raised and lowered
propelled by one bike, left or right side or by the quad
mount for outboard for sandrail and quad
(for returning trips when no vehicle goes back)

4) cataraft frame components need to be broken down for transportation

5) cataraft frame components need to intergrate scuba runabout operation
(submersible bow deck for boat entry, transom for 25 hp outboard)

6) cataraft will also have "dredge" capabilities

7) allow for hovercraft modifications

8) drop down deck floor for bikes and quad

9) sandrail deck on tubes

10) both motorcycle deck rails are adjustable for quad widths

11) single wheel trailer operation for bikes
dual wheel operation for sandrail or quad

12) All vehicles will stay "dry" and out of salt water
during loading, unloading, and underway operations.