Hi franktree and welcome to the forum. A first name would be nice here too some of us wish to be respectful as well as friendly. I'm Hesh and was stuck with it....
Step one that I advise new builders (even of electrics) is to figure out what you need to do where you live to secure a relative humidity solution in your shop. Most of us, there are exceptions shoot for around 42 - 48% as per a "calibrated or checked" quality hygrometer.
It's especially important for acoustic builders but for electrics too. I service guitars for a living and just yesterday had a Strat in with fret sprout, back bow and playability issues all caused by being dry here in Michigan where it's been very cold lately.
Your electric guitars will be more resistant to RH swings without playability issues if they are built in an acceptable RH range. That's why we control RH so that our instruments are more tolerant of swings without cracking or playability issues. And yes even electrics.
Here in Michigan I have to humidify in the winter and dehumidify in the summer.
Now with that said....
1). You don't have to nip the tang and can have it show and many very high quality builders especially of electrics do this. From Martin, Collings, Suhr, etc. it is what we see the most commonly. You can also nip and fill and not bind or bind.
Folks that fill the fret end if there is fret sprout (the guitar dries out) the filling can get pushed proud of the neck and even fall out leaving a cavity. My preference is to run the fret tang to be flush with the neck. If there is fret sprout I have special files that take that back while skating on the finish and not damaging it. No additional filler or refilling required.
2). One of the most common things I see as someone who has endured... here on this forum for nearly 20 years now most of that time helping others is new folks come here with their own ideas how to build a better mouse trap. No offense intended I have seen this countless times and it often gets folks into trouble... We all approach lutherie it seems wanting to be innovative and push the envelope with carbon fiber, new neck joints, you name it. Some of us who end up sticking with it and even making Lutherie a life's choice learn in time to have a very healthy respect for tradition. There are good reasons why guitars such as Martins are assembled as they are - it works. My suggestion to you if you want to innovate is to at least build a few per accepted best practices even if you have to hold your nose and gain more understanding to why we do what we do as we do it. Beware of YouTube videos, Facebook "reels" and such they are major spreaders of bad information on a daily basis. I often repost Facebook reels on my personal page asking my friends what the person is doing wrong here....
Installing binding after finishing it problematic in that it limits any glue you could use to have to not eat finish. You will also have to deal with squeeze out and that is typically scraped off. One scrape too much and you have finish touch up to do.... And bindings benefit from having finish on them too and look better.
Perhaps try it the typical way and then innovate if you want.
3). I never caulked my rods and instead went for a snug fit of the two ends AND I was religious about selecting a quality "double action" rod no matter what the price and then I tested each one in a vice paying attention to the adjustor and it's welds. I built 54 1/2 guitars and never had a problem. I don't see anything wrong with it, caulking but be aware anything with silicon in it can be a nightmare if your shop gets contaminated. Finish will fish eye if it encounters silicon so lutherie shops keep the stuff as contained as possible or don't use it at all.
4). Les Paul made a log that was a stick of sorts where he could move stuff around to learn. If it were me I would again... again let tradition inform me. You have examples that work such as triple pick-up SGs, Strats, and countless other guitars on the market today and can inform your pick-up selection and placement.
A different problem to having in mind, always is that neck angle and pick-ups have a relationship. Be absolutely sure that you get the neck angles correct it the single most important part of building any guitar. Mess that up and you have firewood unless you reset it. So if the pick-ups are too close to the strings you will have intonation problems so be sure there is a full range of height adjustment available.
Lastly who's the puppy? They look great and please pet them for me.
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We have two dogs in our shop now who are on me every day for treats. They are such wonderful souls we could learn from them.
Thanks