: Well aware of the rain issue. I am going to get cockpit covers
: before making any long trips.

And I hope you sew on a few extra loops to those covers so you can tie on safety cords. After they blow off the boat you'll hear them flapping. The air pressure difference when you move at highway speeds can be enough to make replacement covers an annual affair.

: 99% of the time it is just local
: 15-20 minute drives around here. J cradles seem like the easiest
: to load and most adaptable to different boats. I am thinking
: about making a couple of sets to use locally.

Use them for long-distance moves, too. As long as the racks are mounted well why remove them?
They are faster to use on short, around-town trips, too.

: I am sort of leaning toward foam blocks (trimmed to fit) and
: hauling the boats upside down when I head off on a longer trip.

Don't lean too far. Foam blocks are fine for quick moves and when taking the boats on different cars--typically the case with river trips where you park a shuttle car at your takeout point before heading upstream (in another car) to the put-in point. Bow and stern ropes and foam blocks can all store under the deck--and it doesn't matter whose car you use.

But on long trips the combination of road dust, slight shifting of the boat, and the inevitable moisture turn those foam blocks into sanding blocks. On short trips you get some minor scratches you can buff out and wax. After several long rides you get noticeable wear areas on the roof. And as the foam blocks age they trap more grit and do more damage faster.
If you are going to make racks you don't need foam blocks on your car. Just throw them in the boat for paddle floats, or to use on someone else's car in an emergency.

: It would seem to be more aerodynamic at
highway speeds.

Make your racks aerodynamic. They'll lower your fuel economy so you want the best aerodynamics anyhow.

: Might
: make a couple of cradles to hold the boats even. Tossing around
: ideas.

I'm partial to the idera of a low rack with 2 J-cradles near the outside edges. In the center there would be room for 2 bikes, or a 3rd boat. If you come up with something like that I'd like to see it.

Regardless of your rack choice you'll want to add inconspicuous tie-down points under your car. Add a few eyebolts.
PGJ