I just finished the mission that gives you 4 genetarr transmitters. I guess I scrapped two of them at a low level, anyway I can get them back?

Not as far as we know. The best you can do is e-mail Dan using the contact at the bottom of the playing page.

I really wish the special items weren't accidentally sellable. It'd be nice if they had some sort of "lock" feature (same goes for any ship object, to be honest). A confirmation box would work, too.

I know when installed, most NPC mods do have an "are you sure".

It should be like that for items in inventory too, or just make it not scrapable. Some mission items are set that way, but most of them should be really if it's just a small credit value (the tech parts ones I guess have to be).