Congratulations on your new purchase! I would add a couple of points to HStrech's reply.
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Q1: What bad stuff happens if one mirage drive crank set to #4 and other to #5?
Note: Hobie manual says “ensure both cranks are in the same position number.” I was playing around and found flutter strokes with same foot forward easier using different numbers, and I flutter way more than full stroke.
It doesn't hurt at all to use different pin positions as long as you're not slamming the hull with the fins. Using different holes just cuts the range of motion down. For fluttering, I like the #4 and #7 position which keeps the legs almost equal while the fins are operating up near the boat.
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Q3: Are scupper holes or pad-eyes (the bungee cord fasteners) acceptable for a “last resort” safety rope for roof rack transport? If not what else is better?
Note: using roof rack with cross bars & upright bars, I rely 99.9% on straps across the upside down hull, but sometimes put safety ropes (not very tight) on just in case without using front of car. I used small ropes from my roof rack cross bar to kayak pad-eyes. Then saw Hobie manual says “scupper holes to tie the boat to the car is an acceptable method”.
Another way to secure your boat is to run two loops through the drivewell, one to and from each side. They don't have to be tight since there is no way the boat can fall off the rack (snug is good). The scuppers are good as well. The black plastic padeyes are not strong enough for high stress and can pop out, as opposed to the fore and aft stainless padeyes which are screwed in to pre-molded brass anchors.