1 Custodien per full 1000pts, or part of.
I agree on the above post by Kivarn and am still very concerned the fleet is overpowered (Protector, Custodian).
I have given this some thought. How about we take away tracking systems from all ships except the Custodian, make the Custodian's tracking system behave like a Messenger starship, then otherwise leave the Protectors as-is for points but raise the Custodian's cost a notch?
Not opposed.
I personally don't want to revisit the ship profiles anymore. We have burned several weekends and other days playtesting those things to get them tweaked just right against Imperials, Chaos and Orks both before and again after the forum tore our original draft to shreds. They are priced and outfitted well, regardless of what the slide-rules might say. I do find tracking systems a bit of a kick up, but I would rather remove them from Protectors than raise their price.
So you ignore the wish for a fast turning, fixed forward firing (mainly) unique fleet using how the models look like?

Wardens are absolutely not getting 2x30 ion cannon. I don't have any idea how Forgeworld even invented this profile. Well, actually I do, but that's beyond the scope of this post. When the Tau were first being developed and the Games Workshop models weren't even out of the design stage yet, we tested 2x30 ion cannons for the Orca. They were complete and absolute junk against Eldar, and the points they soaked up made the Tau the Eldar's punching bag. On the other hand, it was absolutely ridiculous what they did to Necrons. Anything cheap that turns a fleet into junk against one opponent and poison against another is broken. (Funny side note- because there were no models yet, I used my Space Marines fleet to simulate the Tau. Yes, I know- blasphemy!!) 
First the 2 Ion Cannon Warden is not from Forgeworld. Fanmade design (even I find iffy

, go figure, lol).
Secondly the problem in your playtest was noy the 2IC Warden but the rule system for Eldar. Necrons fear batteries (psychology) as much as lances.
Horizon, I know you hate it, but Emissaries are NOT EVER going to get 90deg turns. They are NOT Tau Dauntlesses. In fluff and our background notes, they were the first of the new Kor'or'vesh designs and are thus less polished than the later Protectors.
Not only me. Look, the ship is smaller then the Dauntless. It has big engines, it has a wing design that even in low orbit it can turn on a dime. Background dictates it is maneouvrable. Background dictates it can run away. Background says it MUST be 90* and 25cm.
As long as the ship stays at 45* it'll be relegated to a gimmick vessel someone takes if he wants to show of a cool model, not for effectivity.
I will continue this crusade, shupported by everyone in this forum (I hope).

The Dauntless tonnage is much higher then the Emissary. The Dauntless is nearly cruiser sized, the Emissary more of an escort.
Even with their evolved tech, Tau are STILL supposed to not be as good as Imperials. Their weapons fit makes them seem like they are, but their weapons are prow heavy, which means they are closing on Imps and Chaos to be effective, while Imps and Chaos are crossing their T to shoot back at them. In actual gameplay, the Tau need all that prow firepower just to stand up to the beating they get against Imps and Chaos.
Then tell me Nate, from Armada:
* Tau have the best carrier force. A cheap battleship, 230pts, that launches 8 resilient bombers. No Imperial Ship can match that. Yes 1:1, but in a fleet duel...
* Tau have better missiles. Faster and Turnable.
* The Tau have the Hero that in a 1:1 duel beats a Lunar, Gothic, Tyrant, Murder, Carnage etc. The fleet limit is just bad rule design to fix this problem.
The Hero costs the same as a Lunar but has much better weaponry. With this ship background and stats go completely false.
As it stands the GW Tau Armada fleet is better then the Imperial Navy by a longshot. Only weakship is the Merchant but it can be avoided to be taken. The only thing Tau might fear is Nova Cannon spam.
Check this, Adepticon winner, twice:
3x Explorer (iirc one was the torp variant, not sure), 2x Hero, 9xOrca, 3xDefender, command.
At warseer a lenghty discussion was applied on what fleet the IN should take in such a tournament setting and both be able to deal with such a Tau fleet, roaming Eldar (non-powergamed as it seemed) and some Chaos. Conclusion was that almost no Imperial Fleet would be able to deal with above Tau list and at the same time have a good day vs Eldar or Chaos for example.
The Prow on weaponry comes only late as the ordnance does the job. And even then : Fighting prow on is much easier then abeam for beginning players.
Short Story: Armada Tau is better then the Imperial Navy. shocker!
This Tau draft will do the same I fear. Certainly as it loses two "weaker" points compared to Armada:
* shooting
* boarding
Both are filled now.
I would rather see the FW Tau fleet as a gunnery fleet overall being light on attack craft (but not so on missiles). Agressive first strike fleet with horrible broadside (unlike draft Tau). Custodian with 4 launch bays, 8 missiles (as per High Admirality original design, yes yes).
I know a lot of people feel like we're just force-feeding rules to the fans. I promise the opposite is true- we made a LOT of changes based on feedback from the forum (gravitic hooks on the Orbital City was particularly well-received). It's just that we put a LOT of effort into making this right while keeping to the designer's intent and true to fluff, and juggling all that is never easy. I want the fans to be happy, but we aren't scrapping this to start from scratch because some people want the Kor'or'vesh to represent something the designers never intended, regardless of how fun it is to play, etc.
So you deny fun and balance to stay in the designer's favour so to say. One could ask themselves if the designers weren't wrong. That might be the case. Designers are never 100% correct. Some even not reaching 10%.

I know we don't agree on everything, but I still want to hear your comments, complaints, etc.
Complaints (with tracking system to Custodian):
* The Aun is still needed on a Protector or is that a typo?
* Aun on Custodian, iffy, not needed.
* As Kivarn pointed out the Protector restriction is a gimmick not doing anything useful
* The 12str battery Protector variant still is better then the 'normal' variant, surely when in companion with Custodian. I advocate a lowering to 8 or max 10 batteries.
* The Railgun Stubs on all models are Fixed Forward, how can I explain to someone they are swivelling?
* I am not opposed to tracking systems on Protectors if the firepower is reduced on the str.12 battery variant to 8. The normal variant has no issues as mighty.
As said, per latest draft the Warden & Castellan are approved of.