Do you have C-3PO? He can make or break a JTR team in either phase -well, just make, really.(and remember, it is a good habit to get into as a guild, especially when you are just breaking into HSTR, to think in percentages of phase, not damage numbers. For example, 10% of phase 2 is 5.2 Million, but 10% of phase 3 is only 3.6 Million - however, that 3.6 million in phase 3 is going to be a MUCH bigger boon to the guild!)
Anyways, if you are running JTR, bb8, R2, Trooper, And scav Rey for that 9-11% of phase 1, you shouldn’t really expect much more than about 4% (1.5M range) in phase 3.
Substitute threepio for scavenger, and you can expect that phase 1 score to go to 14-18% pretty quickly (7-8 Million range), or around 10% of phase 3 (only 3.6M, but the score improves by 250%, as opposed to a 50-70% bump in phase 1).
Can’t really speak to the Embo teams, I haven’t had the resources to dip into him yet, but I am sure somebody else can help there...
More than anything, it is a question of how much ‘spare’ power your guild has -do you have 20 of those JTR teams that can do similar damage to yours for phase 1 (and in the hands of guildies you can count on to be punctual and dedicated enough to restart a run that goes sour)? Then save 5 of them (preferably 3pO teams) for phase 3 (same goes for Revan teams, sure they can rock high teen percentages in phase 2, but spare teams can also knock off 7-10% of phase 3. How about sisters for phase 4? You really only need like 4 Assajj teams to take down Nihilus, so anyone with the Talzin lead zeta could look at running a phase 3 death storm team), because phase 3, as you have discovered, is the real roadblock in the raid...
Anyways, hope that helps, and look forward to hearing that your guild beat the raid very soon!