Definitive S2 CU24 bridge upgrade & set-up questions/advice needed...

[S2C22]

So, most of my upgrades are complete. Bridge pickup is now a Seymour Duncan Custom, and a '59 in the neck, (both chrome-plated). CTS volume pot, 047uf Orange Drop cap, upgraded tone/push-pull pot, and upgraded 3-way blade switch.

Now on to the fun part... I bought a PRS/MANN 2040 2-piece bridge to upgrade that as well. I didn't like the stock bridge, as the saddles tend to shift at string changes, and the "feel" was never consistent in that regard, and I know the MANN is a great upgrade in quality, feel, tone, and tuning, (I'm sure).

I had a block installed in the trem cavity, so it's dive-only. This also allows me to drop-D on the fly, without throwing tuning out of whack, which I much prefer. This prevents any upward movement.
The MANN set-up video he's posted is pretty cut & dry, so no worries on the install. But, I have some specific overall set-up questions:

First, and foremost, the tech that blocked the trem pulled a spring, and only went with 3. I'm sure he had his reasons, but, with a better quality trem/springs going in, should I go back to 4? Of course, I'm after ultimate tuning stability here, even though trem use will be minimal. Light vibrato, partial dives, but certainly no Eddie Van Halen going on here.

Second, I see varying opinions on neck relief in videos. PRS says .010 at the 8th, but some say as low as .005, or happy medium of .007. I definitely find .010 too high for my tastes, but looking for opinions/experiences. I find fret buzz too low, (mainly first 5-6 frets) but also find buzz in the higher registers set too high, (15th or so)? Is this truss rod THAT sensitive?

Lastly - why do I see so many knowledgeable people, (John Mann included), setting intonation with the guitar laying down? I've always been taught/told to do it in the playing position! Am I missing something? In addition, why do some do open string/12th fret note, vs. open string/12th fret harmonic? What's the consensus on that? I've ALWAYS done open/12th harmonic?

Any other tips/tricks to low action/buzz-free set-ups, are much welcomed! I've always done my own guitars, but the 25" scale, and vintage trem-thing is new to me. I'm a wiz with Gibsons, as well as Floyd Roses, but finding the sweet spot in setting this one up has been more time-consuming/challenging.

 

[jak3af3r]

Setting a guitar action while the guitar is laying down is easier.

The intonation thing always gets me because the harmonic is a double of the fundamental so it doesn't matter where the saddle is, if the open string is in tune, the harmonic will be too. I tune, then do a sampling of notes below and above the 12th fret to get it as close as possible to perfect in both zones.

Relief wise, set it up where you find it comfortable. It's YOUR guitar and YOU have to play it.

 

[John Mann]

Both methods can be used. It's the end results that matter.

I do it laying down, but I support the neck of the guitar at the heel, and I make sure not to touch the neck while I am checking intonation.

I do not do it in the playing position because I feel there is more opportunity to introduce unwanted movement of the neck (simply by holding the neck, etc.)