Below is the link to my Fleet Ambassador PVE build.
I also regularly PvP.
As a healer, Damage means very little to me in PvP. If viable equates to damage, the Ambassador is the wrong ship.
I change my lt universal to engineer, and I run 2 x extend shields. I drop the hazard emitter for a sci team. I dump eptw3 for engineer team 3, and run epta/epts1 and always run in full shield mode. Lastly, I take out my plasma infuser consoles(tac consoles)and run universal ones there, I toss in a couple SIF generators into my open engine slots.
With a high aug, I can burst heal for around 9k with aug to sif 3, and 12k with engineering team 3. With the right doff and judicial use of team powers I can pull someone back from the brink of death while they are subnuc'ed and alpha struck.
The current BO layout is;
lt uni : epts 1, et 2
lt tac : faw 1, apd 1
ens tac : tt 1
cdr eng : epts 1, a2sif 1, dem 2, dem 3
ltc sci : he 1, fbp 1, gw 1
Although I've never flown the ship, there are certain universal rules that apply to PvP.
2x TT is preferable (you can run 1x with two purple doffs).
ET is less effective for surviving damage than TT so ET1 is sufficient enough to clear debuffs.
FBP is only good at higher ranks when heavily spec'd in particle generators.
GW is weak at the moment and there are better uses for the LtCmdr sci slot (such as heals).
DEM can be useful but generally you'd do better with one copy of DEM and an additional heal instead of the second copy.
The Fleet Ambassador can also make an excellent dedicated healer as well in place of something like a lockbox ship or an eng-heavy sci ship.
Cmdr Eng: EPTS 1, ET 2, Extend shields 2, Aux to SIF 3 (you can switch Extends to be level 3, and Aux to SIF to be level 2 if you want)
Lt. cmdr Sci: ST 1, HE 2, TSS 3 (or switch for HE 3 and TSS 2, your choice)
Lt tac: Torp spread 1, APD 1
Ensign tac: FAW 1, or another torp ability.
Lt. Universal: Almost anything would do, though I'd recommend science, either to add in another copy of TSS and HE, or to add in a couple things like a tractor beam and maybe a repulsors or something. Or have it be an engineer so you can have EPTA or a second copy of EPTS, maybe along with another extend shields or an RSP.
It has some real usage in the right hands IMO, shame I don't see more of em.