DivaricationOfMind wrote:
Is there are pros or cons to Neoprene bumpers vs. Cork bumpers?
Not really, except that neoprene will last a good bit longer than cork. Assuming you're taking good care of your flute, corks will last for many, many years, but they can be subject to compression (more so than neoprene), and if subjected to moisture or otherwise abused/neglected they are more likely to have issues. However, neoprene is pretty hard in comparison to cork, and some players believe it contributes to mechanism noise. Another issue is tradition (which is pretty big in the music world). Cork has long been the standard material used for the D# key, trill keys, etc, and some people simply don't like the newfangled technology of neoprene.
Do all Yamaha flutes use the same pads?
As Fluttiegurl noted, they all use the same traditional pads (but installed in difference thicknesses and firmnesses, and with different techniques) unless you specifically order a different type for your custom flute. As there's a pretty good used Yamaha market, it's impossible to say what pads might actually be out there on a Yamaha, as some owners will have different pads installed aftermarket.
What are the pros and cons to White Gold springs vs. Stainless Steel springs? Is there any distinct advantage or disadvantage?
There really is no difference between white gold springs and stainless steel, blue steel or any other spring material that you find. It's marketing hype. For a small additional cost for materials, the makers can make it seem as if the flute has an extra feature above and beyond the standard student instrument, and thus can convince people to pay more. The only purpose for the springs is to open (or close) the keys when you release them, and with the proper gauges of spring wire, and the know-how to adjust the tension, any spring wire can be made to perform as you want, regardless of material.
Do custom headjoint cork replacements really make a difference?
Do you mean subsitute stoppers like the Delrin and Zirconium stoppers and crowns from Bigio, etc. or do you literally mean a custom fit head cork of the traditional type? If you mean the substitute stoppers, they can make a difference (though not always a positive one), though this is due less to material than to design. The dimensions of a stopper can make a big difference to the instrument....If you have a larger cork that sits more firmly against the tubing than one you're used to, it may deaden some of the vibrations. However, if the cork is too loose, you will notice a decline in tone and intonation. The same goes for these stoppers. If they suit your flute properly, they may be useful, but if not, then you'll likely hear a negative impact if any at all. Some of these replacements are textured or shaped as well, and this can impact how the flute behaves quite aside from the other issues. The only way to know what difference (if any) these might make to you and your playing is to try them out for yourself with your setup.
Does a mechanisms speed really make that much of a difference when you get to a certain point? considering the keys can't come up before your fingers do, and your fingers can only go so fast.
To very advanced players it does indeed make a difference. The feel of the mechanism under your fingers is very subjective as Fluttiegurl pointed out, but the smoothness (a hallmark of a well-built body), along with the mechanism speed are what sell flute bodies. Even if you hit a wall where your fingers couldn't move any faster, the smoothness and fluidity of technique that's possible with a high quality mechanism matters at the upper levels of playing.
Other than the aesthetics of Pointed Keys, is there any other advantages?
Simply put, no, there are no advantages. They're nice to look at, and provide a flute maker a way to stylize the instrument to suit their tastes (and hopefully the tastes of their customers), but do nothing else. You'll hear it argued that they help maintain equal pressure across the pad cup, meaning pads seal more reliably, but with modern techniques and materials, this is just baseless rumor spread by flutemakers to make you want pointed arms (which generally come only on upper level instruments).
What are the differences between soldered and drawn tone holes, and what are the advantages and disadvantages?

Soldered toneholes are indeed a mark of quality simply for the amount of time that it takes to produce a flute with this method, but they also have another set of advantages. Soldered toneholes are quite a bit flatter at the top than drawn and rolled toneholes (and are easier to flatten using facing tools, should you desire Straubingers or other synthetic pads), which means padding is both simpler, and more reliable. Also, because drawn and rolled toneholes are quite literally pulled out of the tube, they can distort the tubing slightly, which is something that you avoid by having soldered toneholes. Also, some players argue that the sharper edges where the tonehole meets the tubing that are inherent for soldered toneholes leads to faster response. Drawn and rolled toneholes have their advantages, too, though. For instance, they're faster and easier to make (particularly for massed produced instruments), so they are more affordable. As long as they are produced well (so as to avoid overly thin tonehole walls, or tops with large ridges in them), drawn and rolled toneholes are just fine and will certainly do their job. It's a matter of preference and budget, mainly, as soldered toneholes are normally available only on custom built flutes.