Ok, this is pretty wild, but I'd like to propose some radical stats for the Manta.
Given that we have a concensus that the Manta should be more of a troop carrier than a gunboat, to me, the nearest equivilent in Epic is the Marine Landing Craft. They certainly carry a very similar number of vehicles and troops.
It's well known that epic aircraft have artifically reduced DC (see thunderhawk etc), which would put a Manta at about DC5 if it were a bomber. That's pretty close to the Landing Craft. 
So, with that in mind, might it not be possible to at least conceive of the Manta as a bomber rather than the frankly awkward support craft concept?
A weapon downgrade is also fairly agreed upon. I've tried to reflect the 40k weapon layout more closely here, though these are pretty rough stat conversions. Note that in 40k the heavy railcannon is TK(1), whereas other similar weapons (Pylon, Volcano Cannon) are explicitly TK(d3).
Code Sample: 
Tau Manta
Type:         Speed:       Armour:   Close Combat:   Firefight:
War Engine    Bomber       4+        6+              4+
Weapon                   Range          Firepower          Notes
Twin Heavy Railcannons   90cm           MW 2+              TK(1), Fixed Forward Arc
3x Twin Long Barrelled
   Ion Cannons           60cm           AP3+/AT3+          Fixed Forward Arc
8x Drone Targetted 
   Burst Cannons         15cm           AP5+/AA6+          -
Twin Missile Pods        30cm           AP4+/AT5+
Seeker Missiles          75cm           MW6+               Guided Missiles
Damage Capacity 5, Critical Hit Effect: The Manta’s shield control systems are damaged and the
deflector shield fails. It is unavailable for the remainder of the game. Further Critical hits will 
cause an additional point of damage.
Notes: Reinforced Armour, Tau Deflector Shield, Fearless, Planetfall, Transport (may carry 16 of the 
following units: Fire Warriors,Pathfinders, Stealth, Gun Drones, Heavy Drones, Crisis, Broadsides, 
Piranha, Tetra. Note that Crisis units, Piranha and Tetra take up two spaces each. Additionally, up to 
four of the following vehicles may be carried as well: Devilfish,Hammerhead, Swordfish, Skyray, 
Stingray).
Somewhere around the 600 point region?
Thoughts anyone?