I don't think rear facing is a priority, that's more for controlling forward momentum during a crash. You won't be going those speeds very often (or at least should not). Not worrying about rear facing will simplify your engineering solution. But if you think it is important don't let anyone tell you different
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Do have some sort of screen over the kids to protect them from debris in the air and kicked up by your rear tire.
Getting two seats in the trailer will be the tough part. If you make it post pictures of what you came up with.
Awesome that you can sew up a new cover. It is a bit of robbery for what they charge for replacements.