Multiweapon fighting mess
Fiend Folio does a poor job indicating where grafts replace existing body parts, versus adding new ones. For what it’s worth, I always treated long arm as replacing an existing arm, not allowing a new one. It is rather good for its price even so, after all.
Beyond that, there is a question of whether or not the ettin gets any iterative attacks with its off-hand. The description of superior two-weapon fighting does not mention this at all, and the ettin lacks the Improved Two-Weapon Fighting feat which would otherwise be required for “iterative” offhand attacks.
But then the full attack line of ettin’s statblock is wrong... probably? As a creature with BAB +7/+2, the ettin should, assuming it using the two-weapon fighting (and benefiting from superior two-weapon fighting) be making a main-hand morningstar attack at +12, an offhand morningstar attack at +12, and then a single morningstar attack, with either hand, at +7.
What we get is
Full Attack 2 morningstars +12/+7 melee [...]
It’s not all that clear to me if the two morningstars are meant to each get attacks at +12 and +7 (for a total of four attacks, adding an “iterative” to the offhand attack), or if this line isn’t including two-weapon fighting and just shows the +12/+7 that would be the ettin’s base case (which can be made with either of two morningstars). The former contradicts the text insofar as the text offers no way for the ettin to get that iterative, and the latter is just useless and unhelpful. Either seems like a mistake to me, but I can’t decide what, exactly, the ettin is supposed to have here.
However, if you rule that superior two-weapon fighting silently offers the benefit of Improved Two-Weapon Fighting, or even Perfect Two-Weapon Fighting, and that long arm adds new arms rather than replacing old ones, then I would say that the superior two-weapon fighting benefits should apply to all four arms, too. Multiweapon Fighting says it “replaces” Two-Weapon Fighting for creatures with more than two arms, and Perfect Multiweapon Fighting likewise says it “replaces” Perfect Two-Weapon Fighting. What that means is massively unclear, but as I’ve laid out elsewhere, my opinion is it means that the distinction between two-weapon and multiweapon options should be ignored entirely. It adds nothing but horrific confusion to the game. I would apply that to superior two-weapon fighting just as I would to Two-Weapon Fighting et al.
About that “independent action” blurb
Fiend Folio’s description of the long arm graft includes this:
Though it cannot take independent action, the arm can be used to make natural attacks,
and no one knows what it means. “Independent action” isn’t a defined game term, and read as plain English, it might mean any number of things, so it’s not really at all clear what this arm cannot do for lack of it.
The most straightforward/literal interpretation, that I tend to go with, is that this is a statement that the long arm doesn’t have its own set of actions to attack with, and doesn’t automatically attack on your turn while you’re doing other things—which is a feature some options do have. For example, the living whip symbiont from Eberron Campaign Setting. But note that Eberron Campaign Setting was published many years after Fiend Folio, and none of the grafts in Fiend Folio have this feature—which makes you wonder why, if this is what they meant, they felt the need to include the line. Even if it weren’t there, there is nothing to suggest that the long arm would have that ability anyway.
But nonetheless, I think this interpretation simply makes the most sense and leads to the least problems in game. Trying to deny the long arm the ability to, say, wield weapons, doesn’t really make sense—the book would probably say that if that were what was meant, and in any event that doesn’t involve “independent action” any more than it does for your original arms.
It might mean that you cannot use your long arm and your original arm (arms?) in the same round—that the addition of a new arm doesn’t give you the brain capacity to direct more arms. Except with practice, you ought to, and in any event, again, if that was what they meant, they would probably say that and not this thing about “independent action.”
Another possibility is that they mean that the arm needs to work in conjunction with one of your original arms. In other words, it can allow you to do something two-handed or three-handed or whatever, where otherwise you wouldn’t have enough limbs to do that, but it cannot do anything one-handed on its own. Except that makes no sense—the entire point of the long arm is to have greater reach than your original arms, which you wouldn’t be able to use if the long arm was forced to act in conjunction with your original arms.
Anyway, assuming that the long arm is in addition to your original arms rather than instead of, it seems to me that the most reasonable interpretation of this line should have no impact on the ettin’s ability to quad-wield weapons.
This, at least, is clear enough: reach weapons double your natural reach. With the long arm graft, your natural reach is 5 feet longer than it otherwise would be. Therefore, when a long arm wields a reach weapon, that gets doubled too—the spinning swords wielded by the long arms should have 30-ft. reach.
Reversing the order of operations is nonsense, because it would require the benefits of long arm to apply after those of the reach weapon—literally impossible since the long arm has to be in place and granting its benefit before it can pick up a weapon.
As an aside, though, for the record: if you went with a whip, or meteor hammer or rope dart, and then asked this question, no one would be able to help you, because the rules just never explain how the whip’s 15-ft. reach for Medium creatures works. See my answer to this Pathfinder question, noting that unlike Pathfinder, 3.5e lacks even a developer stating a quasi-official opinion on the matter.