The longer rectangular box that is mostly painted over is a super-old Winegard TV distribution amplifier (as someone suggested above). Here is almost the exact same one, I'm pretty sure: https://www.ebay.com/itm/Winegard-DA-8150-82-Channel-Distribution-Amplifier/193941261031?hash=item2d27cccae7:g:SZEAAOSwxjZgRUNJ The other box that is completely painted, with the two connections at the top and power coming out of the bottom, I think is one of these: https://www.ebay.com/itm/303839191777?mkevt=1&mkcid=1&mkrid=711-53200-19255-0&campid=5338722076&toolid=10001 a pre-amp TV signal booster, effectively similar to the longer box. But, those boxes utilize coax cable-TV-style cable, and the intercom amplifier uses thinner, twisted pair wires that are orange red and black. The cable going into the antenna device in the closet appears to have a larger, heavier gauge wire with green, black, and red conductors....I would try to trace that specific cable as far as you can and see where it goes first. Were there any other kind of junction boxes underneath the house? The intercom amp appears to have a line coming into the DOOR input, one line going to the regular input and one line going to the output terminals, which would suggest that they likely just had one door speaker, and one inside speaker to communicate with the front door. If you had multiple intercom speakers throughout the house, typically you would have multiple wires going to those terminals, but I do believe those particular nutone systems could be "daisy-chained" as well, with one room station wired to the next, in a line, etc...so it is possible there could have been more. I am absolutely fascinated by what this thing in your closet could be! If it is, in fact, somehow wired into one or both of those two TV distribution amps, maybe it was some kind of project idea from Popular Electronics that utilized making your own antenna and using those amps to power it somehow, but I just can't imagine why you'd have it in a closet, it is so intriguing. The key-switch on the wall looks very common to many old alarm systems of the time, but typically you'd have other security system components around, like sensors on your doors/windows, and a siren mounted somewhere outside your house...It is also entirely possible that the TV distribution amp boxes underneath the house were not related to that antenna thing, but it seems like it would be too much of a coincidence, especially since someone wrote "closet" down there on the joist. This three-year-old mystery is so damn interesting! haha

Would be tempted to drop the linen closet light. But how to combine the lights depends a lot on the amount of space and where they'll be placed -- e.g., could the vanity lights be the main thing you use everyday? if so, then combining cans and fan (with a split) might be a good solution.

Thanks for the help and suggestions with the photos. The beam will be just as low as it it now. It would just be about a third narrower. I got it about the recessed lights over the island, but I was wondering if there is any way to make this more decorative too? Also, would that be enough to light the whole kitchen (except the eating area)? Any advice on how many lights or how strong they should be? The kitchen will have a reddish brown hardwood and white cabinets. Mostly existing appliances. Also, we just put LED recessed lights in another room and they just don't dim enough. Any thoughts on lights that actually dim? Stick with incandescents or try something else? Thank you!!

Go with your first choice. It is more practical for usage purposes and will probably look the best.