Never tried the Al Green tune...
I would leave the finish alone. It might sound different, I don't know about better..
Pickup height - I have to set mine on my strat, all stock single coils, high as they will go then tweak to get volumes even. I also drop the treble end a little lower, they tend to get too much treble if I don't. Humbuckers will probably be different, they usually aren't as bright as single coils.
When you set the intonation use new strings. Doing it with old strings is wasting your time. Set the action and get the bridge right first.
Use a #2 pencil in the nut if you have any intonation problems due to the tremolo, I've used it for 20 years and it does the trick.
The bridge should be set so it floats slightly above the guitar body, about 1/32 inch, and level with it. (My Peavey is different, I looked it up and Peavey says set it to a 10° angle) I loosened the 4 middle screws on mine to let it float better and use only the 2 outside end screws to hold it. Some Strats are set up this way from the factory, they only have 2 screws instead of the 6 others have.
Other tweaks and maintenance - A drop of light oil on each tuner (down the side of the tuner post so it gets inside to the gears) every couple of string changes helps keep them in good shape. (3 in 1 or sewing machine oil, NEVER any kind of penetrating oil on any guitar.) A toothpick and a bit of wood glue does a great job of fixing loose strap pegs. I've had to do the pegs on every guitar I have at least once. Keep the screws and tuner post nuts snug but not really tight. It's easy to strip the small screws on back, and if any get loose it can lead to tuning problems. The toothpick trick works for any screw on the guitar. Keep the screws on the back plate at the back of the neck tight. If they get loose the neck can move around. (caused one of mine to get really flaky about holding tuning once. Push it a little and it would change.) Took me a month to figure it out.
A drop of oil on the truss rod nut about once or twice a year will keep it from getting rusty and locking up. Nothing will ruin your day like trying to adjust a truss rod and snapping it because the threads were rusty and locked in place...Never touch the truss rod unless it definitely needs it and you KNOW how to adjust it properly. And ignore anyone who tells you it has anything to do with action or intonation, Those are myths. The truss rod has one purpose and one only. To maintain the proper "back bow" of the neck so the strings have room to vibrate in the middle. It should only be adjusted if the back bow is not right. It will not affect intonation and only has a very very slight affect on action. If it needs adjustment you won't know it by the action. Usually it will be because it buzzes in the middle of the neck.
A fine grit foam fingernail board can help remove burrs on bridge saddles, or a folded piece of fine grit sandpaper. Those burrs can drive you crazy breaking strings. I use something I got in machine shops called craytex, (cratex?) it's rubber similar to a pencil eraser impregnated with diamond dust. If you can get some it's excellent for removing burrs on saddles and frets. I keep a piece in my spare string bag along with a #2 pencil to put some graphite on the nut slots when I change strings.
Or bring it to me and I'll have it in top condition in a day or two. I've been working on them for at least 20 years...the only thing I haven't tried is replacing frets...
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If you see me running, better catch up!